JPH06309385A - Constructing method for molecular structure for ligand having bioactivity - Google Patents

Abstract

PURPOSE:To obtain a method by which the molecular structure of a new ligand can be automatically constructed by holding the position and direction of a specific functional group existing in a ligand molecule, appropriately arranging an atom in a permitted space, and comprehensively retrieving a connecting path. CONSTITUTION:At first, receptor mapping is operated based on the molecular structure of the known ligand by, for example, the method of a RECEPS, three-dimensional lattice point information is obtained, and the inside hole model of a receptor is constructed. Next, the functional group of the known ligand molecule which is important to an interaction with the receptor is extracted by, for example, the method of a LINKOR, the position and direction of the functional group are designated, and the molecular structure of the new ligand can be constructed while the position and direction of the functional group are held. Also, O-H, N-H, and benzen ring are the function group extracted from the molecular structure of the known ligand which is important to the interaction with the receptor, and (a) indicates the inside hole model of the constructed receptor by the receptor mapping operated based on the molecular structure of the known ligand by using the RECEPS.

Description

Detailed Description of the Invention

[0001]

TECHNICAL FIELD The present invention relates to a method for constructing a molecular structure of a compound having physiological activity, and more specifically,
The present invention relates to a method for automatically generating a molecular structure of a novel compound, which can be used for designing a molecular structure of a drug, a pesticide or other compound having a physiological activity.

[0002]

There are two conceptual steps in drug design. It is the process of lead creation that finds the compound (called lead) that will be the starting point for subsequent drug development, and the process of lead optimization that finds compounds that are more active and have less toxicity and side effects starting from that lead. A lead is a compound known to have a certain physiological activity of interest, and is also called a lead compound. Most of the commonly used drug design is this second step, often by synthesizing a series of substituent derivatives from known active compounds and comparing their activities. It is extremely difficult to artificially perform the first step, and it is discovered from natural substances, from the side-effects of known drugs, structural modifications from bioactive substances (neurotransmitters, hormones, vitamins, etc.), Or, as soon as possible, the available compounds will be discovered by random screening using a prepared evaluation system.
Much depends on chance, good luck, and trial and error. Starting with an appropriate lead influences the success or failure of drug development thereafter, and since there are many diseases where good drugs cannot be obtained because there is no appropriate lead, it is necessary to develop a method for obtaining highly active leads with a high hit rate. This is widely desired. What pharmacological activity a compound exhibits depends on which receptor (biopolymer) it binds to, but one compound does not always bind to only one receptor. Therefore, the strength of the main activity and the side activity (side effect) may be reversed or the activity may disappear due to a slight difference in structure. Also,
Even if the main activity does not change, the behavior in the body, such as the ease of metabolism and the interaction with the membrane, greatly changes, often affecting the properties as a drug. Furthermore, it is expected that drugs from new leads with different molecular skeletons will show completely different behaviors even if they have the same main activity.

In order for a drug to exert a physiological activity, it must reach a certain site of the receptor in the body and specifically interact with the receptor (usually a strong non-covalent association).
In recent years, the technology of isolating and purifying the receptor has advanced, and more and more three-dimensional structures (three-dimensional coordinates of constituent atoms) of enzymes and nucleic acids have been elucidated by X-ray crystallography. In particular, from the analysis of the complex with the ligand (inhibitor in the case of an enzyme), a strong van der Waals interaction is observed between the ligand molecule that shows strong binding and the receptor due to the good fit of the molecular surface shape. It is known that hydrophilic interactions such as hydrogen bonding and electrostatic interaction contribute to stabilization of the complex. Despite the fact that the apparent structure is completely different from that of the active substance or enzyme substrate that originally works in the living body, binding to the same receptor was confirmed, and there are many drugs that have the same action or inhibitors. From this, it is understood that the strong binding between the receptor and the drug requires the three-dimensional shape of both molecules and the complementarity of these properties. Therefore, if humans can design a molecular structure having a three-dimensional structure that meets these requirements, it should be possible to artificially create leads. However, since it is easy for humans to get caught up in the structures of known active compounds and they are not good at three-dimensional insight, it is difficult to create leads even when the three-dimensional structure of the receptor is elucidated by crystal analysis. Therefore, an approach in which such a structure is presented to a computer and a human selects from it is considered to be effective in finding a new active structure and leading it. Computers are not prejudiced, cover possibilities, and provide quantitative evidence-based results.

There are two possible approaches for finding a structure that meets the conditions required for the lead.
It is a method of searching a structure of a known compound for a structure satisfying a condition, and a method of newly constructing a structure satisfying such a condition. When the three-dimensional structure of the receptor is available, there are the following reports on both approaches.

Des Jarlais, Kuntz et al. Have described the shape of the inner pore of the drug binding site with several spheres that fit well in it, and have made a crystal database (published by the University of Cambridge, UK: more than 100 scientific fields around the world). Each compound in (registered analysis reported in the journal),
We announced a method (DOCK) to judge the similarity of the receptor to the set of spheres by expressing it with several spheres containing it (R.
L. DesJarlais, RPSheridan, GLSeibel, JSDixo
n, ID Kuntz and R. Venkataraghavan, J. Med. Che
m. 31, 722-729 (1988); RL DesJarlais, GL Seibe
l, ID Kuntz, PS Furth and JC Alvarez, Proc. N
atl. Acad. Sci. USA, 87, 6644-6648 (1990)). This method is applied to the AIDS virus proteolytic enzyme (HIV protea
se: registered in the Protein Data Bank), the crystal structure of a compound called haloperidol, which is known as a beta-blocker and antipsychotic, was chosen as a good fit for the drug-binding site of this enzyme, and minor structural modifications were made. When it was synthesized and examined for activity, it was proved to be effective for treating AIDS by inhibiting this enzyme. However, this method judges only the shape of the molecule, does not consider hydrogen bonding and other interactions, and also considers only the crystal structure of the molecular conformation.
Leakage and inefficiency of promising candidate compounds are problems.

Also, Lewis et al. Assume a diamond lattice in which the side length is the length of a carbon-carbon single bond at the drug binding site, and a carbon atom is appropriately placed on the lattice point to newly establish a molecular structure. Announced how to build (RA Lewis, J.
Comp.-Aided Molecular Design, 4, 205-210 (199
0)). However, in this method, atoms other than sp ³ hybrid cannot be installed, and specific interaction with the receptor is not considered at all, and it is not practical.

Nishibata and Itai et al. Have published a method for assembling a structure that fits well to the drug binding site of the receptor and have a stable interaction, and a program LEGEND for implementing this method (Y. Nishibata and A. Itai, Tetrahedron, 4
7, 8986-8990 (1991)). This method is a method of adding atoms or atomic groups one by one based on random numbers and force fields so that van der Waals interactions with receptors, hydrogen bonds, and electrostatic interactions become advantageous. . It excels in suggesting a large number of possible structures, but it has been proved to be effective in application, but actual success cases have not yet been confirmed.

Bohm developed a method for constructing a novel structure by fitting several appropriate ones out of a large number of fragment structures prepared in the program into the drug binding site of the receptor and ligating them well. (H.-J. Bohm, J. of Co
mp.-Aided Molecular Design, 6, 61-78 (1992)). However, the result which proves the effectiveness of this method is not yet obtained.

If the three-dimensional structure of the receptor is not known, the above two approaches cannot be used.
Another approach is needed. The number of biopolymers for which the three-dimensional structure is currently announced is about 1,000, including those derived from bacteria, and it is necessary to determine the structure of each human receptor, which is said to exist in the body in the tens of thousands. Is expected to take many years. Therefore, an approach method for constructing the structure of an active ligand molecule when there is no information on the three-dimensional structure of the receptor is currently required.

When there is no information on the three-dimensional structure of the receptor, the most effective method for finding the structure-activity relationship from the side of a ligand molecule such as a drug, a physiologically active substance or an in-vivo active substance is the superposition of molecules. It is a match. Multiple compounds that bind to the same site of the same receptor and exert similar physiological effects (though if they have similar molecular structures, they will not overlap)
Must have common characteristics in shape and intermolecular interaction, and the common characteristics can be extracted by superimposing those molecules three-dimensionally. In addition, the determination of the molecular conformation (called the active conformation or active conformation) when a molecule having a rotatable single bond in the molecule binds to the receptor and expresses an activity is also determined. Made possible by In addition, estimating the environment and size of the drug binding site of the receptor from the ligand side is called receptor mapping, and such estimation is called a receptor model. This receptor mapping can be effectively performed based on the superposition of molecules.

There are various methods of superimposing molecules, but the superimposition results vary greatly depending on the method, and different structure-activity relationship models and receptor models (estimation of functional groups considered necessary, shape of drug-binding site of receptor, etc.) can be obtained. Or estimate the nature and environment). In order to arrive at the correct model as possible, the use of logical superposition methods is essential.

As a method of superposing molecules which has been generally performed so far, two or more corresponding pairs of atoms are designated based on the molecular skeleton and the similarity of the positions of heteroatoms.
It has been practiced to superimpose them by least squares calculation so that the positions of the molecules match each other best, or to appropriately superimpose them by visually judging them on a computer graphics screen.

However, in the superposition of molecules of a plurality of drugs or physiologically active substances that bind to the same receptor, Itai and Kato et al. Have atomic positions (molecular skeletons) between the superposed molecules.
The shape of the molecule, hydrogen bonding,
A method of superposing molecules in which electrostatic properties and other physical and chemical properties are the same among the superposed molecules (RECEP
S) was devised and announced. (Y. Kato, A. Itai and Y.
Iitaka, Tetrahedron, 43, 5229-5236 (1987); A. Itai,
Y. Kato, N. Tomioka, Y. Iitaka, Y. Endo, M. Haseg
awa, K. Shudo, H. Fujiki and S. Sakai, Proc. Natl.
Acad. Sci. USA, 85, 3688-3692 (1988); Y. Kato, A. I
noue, M. Yamada, N. Tomioka and A. Itai, J. Comp.-
Aided Molecular Design, 6 in press (1992); A. Ita
i, N.Tomioka, Y. Kato, Y. Nishibata and S. Saito,
in'Medicinal Chemistry in21st Century ', edited by
CG Wermuth, Blackwell Scientific Publishings, Lo
ndon, (1992) in press; A. Itai, N. Tomioka and Y. K
ato, in 'QSAR: Newdevelopments and Applications',
edited by T. Fujita, Elsevier Science Publishers,
Amsterdam, (1992), in press.) Using this RECEPS, the molecules can be interactively moved and rotated on the computer graphics screen using the agreement between the molecules of these properties as an index, while changing the conformation. It became possible to obtain a superposition. This allowed for the first time superposition of molecules with apparently different chemical structures.

Then, in a system in which hydrogen bonding plays an important role in this RECEPS, the computer automatically creates a superposition structure in which the positions of hydrogen bonding functional groups expected from the plurality of molecules to the acceptor side are aligned. Added a function that covers and ranks and shows. With this improvement,
Now, it is possible to obtain objective and correct overlaying results that cover various possibilities derived from overlaying methods and conformations.

Using the molecular superposition method as described above,
When the three-dimensional structure of the receptor is unknown, it has become possible to extract features that are common to multiple ligand molecules with completely different structures. The method of designing a new ligand molecule based on this information and creating a lead has not yet been established, since the relationship between the activity and the activity is postscriptly explained.

[0016]

Accordingly, it is an object of the present invention to provide a method for constructing a novel active ligand molecule structure based on the known active ligand molecule structure. It is another object of the present invention to provide a method for constructing a novel active ligand molecule structure based on the known receptor molecular structure.

[0017]

DISCLOSURE OF THE INVENTION As a result of diligent efforts, the inventors of the present invention have maintained the position and orientation of a specific functional group present in a ligand molecule within a space that is considered to be acceptable for the molecule. At the same time, we have developed a method to automatically construct a molecular structure of a novel ligand by comprehensively searching for binding pathways by appropriately arranging atoms in space,
We have succeeded in solving the above problems.

That is, the present invention provides a method for constructing a molecular structure of a ligand having physiological activity, which comprises (i) extracting two or more functional groups presumed to be essential for the physiological activity of the ligand, First to specify the position and direction of the functional group
A step, (ii) a second step of setting the connection method between the functional groups extracted in the first step, (iii) a third step of specifying the number, type, and existence region of atoms connecting the two functional groups, (iv) disposing a probe atom in the inner hole of the receptor of the ligand,
When the position of the probe atom satisfies a predetermined condition,
Fourth step of adopting as a position of an atom connecting two functional groups, (v) Repeating the fourth step for all atoms specified in the third step creates a bond path between the two functional groups. By combining the binding pathways obtained by repeating the third to fifth steps for all the combinations of the two functional groups set to be connected in the second step, and (vi) the second step. ,
A sixth step of forming a skeleton of the ligand molecule,
The above method is provided.

The fourth step may be carried out by arranging probe atoms on a three-dimensional lattice point, or the probe atoms may be present at points on the circumference where the bond atoms can be calculated from the bond distance and the bond angle. You may do by arrange | positioning an atom. In addition, the present invention provides a method for constructing a molecular structure of a ligand having physiological activity, wherein (i) based on the molecular structure of one or more known ligands, the receptor for the ligand is obtained by obtaining three-dimensional lattice point information. Step (ii) extracting two or more functional groups presumed to be essential for physiological activity from the molecular structure of the known ligand, and determining the position of the functional groups. Second to specify the direction
A step, (iii) a third step of setting the method of connecting the functional groups extracted in the second step, (iv) a fourth step of specifying the number, type, and existence region of atoms connecting the two functional groups, (v) A fifth step of arranging a probe atom in the inner hole of the receptor and adopting it as a position of an atom connecting two functional groups when the position of the probe atom satisfies a predetermined condition, ) A sixth step of creating a bond path between two functional groups by repeating the fifth step for all the atoms specified in the fourth step, and (vii) setting to connect in the third step The method as described above, which comprises a seventh step of forming the skeleton of the ligand molecule by combining the binding pathways obtained by repeating the fourth to sixth steps for all combinations of the two functional groups described above. Is provided.

Further, the positions and directions of the functional groups specified in the above-mentioned second step are sequentially specified again in the positions and directions in which it is presumed to have the same effect, and the above third to seventh steps are repeated. Good. Further, the functional groups extracted in the second step may be sequentially replaced with other functional groups having equivalent physicochemical properties, and the third to seventh steps may be repeated.
Furthermore, the present invention, in addition to the first to seventh steps, (viii) determines whether or not there is an atom whose valence is not satisfied in the molecular skeleton of the ligand, If it exists, it is judged whether or not it is necessary to form a ring structure in the molecular structure of the ligand by the eighth step of adding a hydrogen atom to the atom, (ix) predetermined conditions, and if necessary, The present invention provides a method for constructing a molecular structure of a ligand having physiological activity, which comprises a ninth step of forming a ring structure, and (x) a tenth step of optimizing the molecular structure of the ligand.

According to the method of the present invention, a known ligand molecule exists, but a novel ligand molecular structure can be constructed even when the receptor structure is unknown. Furthermore, the present invention provides a method for constructing a molecular structure of a ligand having a physiological activity, comprising: (i) based on the structure of a known receptor of the ligand, the three-dimensional lattice points of the three-dimensional lattice points created in the inner pore of the receptor. A first step of obtaining information, (ii) a second step of extracting two or more functional groups that interact with the receptor from a functional group in a known ligand molecule, and designating the position and direction of the functional group; (iii) a third step of setting the connection method between the functional groups extracted in the second step, (iv) a fourth step of specifying the number, type, and existence region of atoms connecting the two functional groups,
(v) A fifth step of arranging a probe atom in the inner hole of the receptor and adopting it as a position of an atom connecting two functional groups when the position of the probe atom satisfies a predetermined condition,
i) A sixth step of creating a bond path between two functional groups by repeating the fifth step for all the atoms specified in the fourth step, and (vii) connecting in the third step. For all combinations of the set two functional groups, including the seventh step of forming the skeleton of the ligand molecule by combining the binding pathways obtained by repeating the fourth step to the sixth step, It provides a method. According to the method of the present invention, a novel molecular structure of a ligand molecule can be constructed even when the structure of the complex of the receptor and the ligand molecule is elucidated.

Furthermore, the present invention provides a method for constructing a molecular structure of a ligand having physiological activity, comprising: (i) a tertiary structure prepared in the inner pore of the receptor based on the known structure of the receptor for the ligand. The first step to obtain the information of the original lattice points, (i
i) a second step of selecting two or more functional groups capable of interacting with the receptor and designating the position and direction of the functional groups, (iii)
A third step of setting the way of connecting the functional groups selected in the second step, (iv) a fourth step of specifying the number, type and existence region of atoms connecting the two functional groups, (v) the acceptance A fifth step of arranging a probe atom in the inner pore of the body and adopting it as a position of an atom connecting two functional groups when the position of the probe atom satisfies a predetermined condition, (vi) the fourth step Repeating the fifth step for all the atoms specified in Step 6 to create a bond path between the two functional groups.
Step, and (vii) For all combinations of the two functional groups set to be connected in the third step, the binding pathways obtained by repeating the fourth step to the sixth step are combined to combine the ligand The above method is provided, which includes a seventh step of forming a molecular skeleton. According to the method of the present invention, even when the structure of the drug binding site is elucidated by the structural analysis of the receptor alone, or the structure of the complex of the receptor and the ligand molecule is elucidated, the novel ligand The molecular structure of can be constructed.

Further, the present invention provides a method for constructing a molecular structure of a ligand having physiological activity, which comprises (i) creating atomic coordinates of one or more known ligand molecules and the inside pores of the receptor for the ligand. And (ii) extracting two or more functional groups presumed to be essential for physiological activity from the structure of the known ligand molecule, and The second step, which specifies the position and direction of, (i
ii) a third step of setting the connection method between the functional groups extracted in the second step, (iv) the number and type of atoms connecting the two functional groups,
And a fourth step of designating an existing region, (v) arranging a probe atom in the inner hole of the receptor, and if the position of the probe atom satisfies a predetermined condition, an atom connecting two functional groups A fifth step adopted as a position, (vi) a sixth step of creating a bond pathway between two functional groups by repeating the fifth step for all atoms specified in the fourth step, and (vii ) For all combinations of the two functional groups set so as to be connected in the third step,
The method includes the seventh step of forming the skeleton of the ligand molecule by combining the binding pathways obtained by repeating the steps to the sixth step. As the atomic coordinates of the ligand molecule input in the first step, it is possible to use the atomic coordinates of a known single recand molecule or the atomic coordinates of the ligand molecules that are superposed on each other on the assumption of interaction with the same receptor. it can.

In the present invention, the term "receptor" refers to all biopolymers that can be targeted by drugs, and includes proteins, nucleic acids, polysaccharides, and complexes thereof. A ligand is a low-molecular-weight compound (about 1,000 or less) that strongly binds (interacts) with a specific site of a specific receptor, and is a bioactive substance such as a neurotransmitter, hormone, or vitamin, or a natural substance. And synthetic bioactive substances, drugs, enzyme substrates and the like.

The functional group means an atom which is considered to have a specific function in a chemical reaction or molecular recognition, or an atomic group (atomic group) which always acts as a group. For example, an amino group, a nitro group, a benzene ring and the like can be exemplified. The direction of the functional group means the direction capable of interacting with the receptor. In the case of a functional group that bonds with hydrogen, the direction of the lone pair or hydrogen is taken, and in the case of an aromatic ring such as a benzene ring, the direction of π electron perpendicular to the ring is taken as the direction of the functional group.

The probe atom refers to a temporary atom to be placed in the pore of the receptor in order to determine whether or not a certain position in the pore of the receptor is appropriate as the position of the atom constituting the ligand molecule. And The three-dimensional lattice point information represents the receptor model spatially and position-dependently,
The data is the data stored by calculating the information of the environment of the receptor at each position on each grid point with the grid interval of about 0.2 to 0.5 angstrom. Three-dimensional grid point information is
For example, an address indicating a spatial position for each lattice point, occupancy information by each ligand molecule (up to 6 molecules), electrostatic potential, whether or not a hydrogen-bonding functional group is predicted, and if so, its property is hydrogen. It includes data such as whether it is a donor or acceptor and whether the aromatic property is a problematic position. The occupancy information by the ligand molecule is a lattice point indicating whether or not the three-dimensional lattice point is within the region occupied by the ligand molecule, that is, within the region included in the van der Waals radius of the atoms constituting the ligand molecule. It is information for each. By using this three-dimensional lattice point information instead of the three-dimensional structure of the receptor, it is possible to construct the molecular structure of the ligand while rapidly determining whether or not it matches.

[0027]

Industrial Applicability According to the method of the present invention, a novel ligand compound having physiological activity can be predicted with high probability. Further, the method of the present invention enables high-speed molecular design of a novel ligand compound having physiological activity.

[0028]

1 illustrates the concept of the method of the invention. In the method of the present invention, first, for example, by the RECEPS method, receptor mapping is performed based on the molecular structure of a known ligand, three-dimensional lattice point information is obtained, and an inner pore model of the receptor is constructed, and then, For example, by the LINKOR method, a functional group of a known ligand molecule that is important for interaction with a receptor is extracted, the position and direction of the functional group are designated, and the position and direction of the functional group are preserved. The molecular structure of novel ligands can be constructed. O in FIG.
The -H, N-H, and benzene rings are functional groups extracted from the molecular structure of known ligands that are important for interaction with the receptor. In addition, a schematically shows an internal pore model of the receptor constructed by receptor mapping using RECEPS based on the molecular structure of a known ligand.

FIG. 2 illustrates the method of attachment between two functional groups that can be used in the method of the present invention. The method of the present invention comprises two coupling methods, which can be selected at the time of use. FIG. 2 shows a method of connecting the functional group A and the functional group B with three atoms of a, b, and c. In bonding method 1, atoms a, b, and c are taken on a three-dimensional lattice point. In FIG. 2, dotted lines derived from A and B and a and b indicate bond distances, and arrows derived from A and B indicate directions of the functional groups A and B.

In the bonding method 2, the atoms a, b and c are taken not on the three-dimensional lattice points but on the circumference where the bonding atoms can exist calculated from the bonding distance and the bonding angle. Yen (a),
(b) and (c) show candidates for the existing positions of the atoms a, b, and c, respectively. FIG. 3 shows a method for forming a ring structure in the present invention. In FIG. 3A, in step L30 of the flowchart of FIG. 5 described later, one carbon atom is placed at the center of two hydrogen atoms according to a predetermined condition,
This carbon atom is bonded to the carbon atom bonded to each hydrogen atom to evaluate the bond distance, bond angle, and dihedral angle, and if this is within the allowable range, a method for forming a ring structure is schematically shown. To indicate. FIG. 3B shows FIG. 5 described later.
In step L33 of the flowchart of FIG. 3, a portion where the ring structure is more stable due to interatomic contact including a hydrogen atom is searched for, and the hydrogen atom is converted into a carbon atom while considering the bond length, the bond angle, and the twist angle. A method of forming a new ring structure after substituting with an atom is schematically shown.

4 and 5 show the use of LINKOR,
3 shows a flow chart of one embodiment of the method of the present invention. Details will be described later. FIG. 6 shows a flowchart of a molecular superposition method using RECEPS and receptor mapping. FIG. 7 shows the concept of molecular superposition method using RECEPS and receptor mapping. RECEP
There are two S molecular superposition methods: an interactive superposition method and an automatic superposition method. By superposing the molecular structures of known ligands by the interactive superposition method or the automatic superposition method, and by optimizing the superposition model in consideration of other properties, three-dimensional lattice point information (shape property, Receptor mapping represented by information such as hydrogen bondability, electrostatic potential, and aromaticity) is performed. RE
The CEPS method is characterized by performing molecular superposition considering the interaction with the receptor and performing receptor mapping using three-dimensional lattice point information.

FIG. 8 shows the chemical structure (a) and crystal structure (b) of morphine, and the position and orientation (c) of the extracted functional groups (benzene ring and protonated nitrogen). Also, a
Indicates the wall of the receptor. FIG. 9 (a) shows a morphine receptor model expressed using three-dimensional lattice points. The space surrounded by the cage represented by the diagram shows the inner hole of the receptor. Further, FIG. 9 (b) shows the position of the anionic or hydrogen-bonding heteroatom expected on the acceptor side.

FIG. 10 is obtained by the method of the present invention,
A part of the molecular structure of the ligand of the morphine receptor is shown. The framed molecular structure is the same as the molecular skeleton of compounds already known to have analgesic activity. FIG. 11 shows
The molecular structures of compounds having the same molecular skeleton as the molecular structure of the ligand obtained by the method of the present invention and already known to have analgesic activity equal to or higher than that of morphine are shown.

FIG. 12 shows the structures of known inhibitors analyzed by X-ray crystallography along with the bacterial protease proteolytic enzyme lysopath pepsin. Pro is proline, Phe is phenylalanine, His is histidine, Val is valine, Ty
r indicates tyrosine, and Ψ [CH ₂ —NH] indicates that the peptide bond C0NH at this portion is CH ₂ NH. In the upper row, the structure of the inhibitor of lysopath pepsin is represented by the amino acid sequence. In the lower part, the chemical structure and the three-dimensional structure of the boxed portion in the amino acid sequence of the inhibitor of lysopathpepsin shown in the upper part are shown. In the chemical structure of the inhibitor, the five functional groups that interact directly with the substrate binding site of lysopath pepsin are circled and numbered.

FIG. 13 is obtained by the method of the present invention,
The molecular structure of the ligand of lysopath pepsin is shown (output 1
~ Output 11). FIG. 14 shows a state in which the molecular structure of the ligand of lysopath pepsin (shown in the output 9 of FIG. 13) obtained by the method of the present invention is arranged in the inner pore containing the substrate binding site of lysopath pepsin. Indicates. In FIG. 14, the thick line represents the molecular structure of the ligand of lysopath pepsin obtained by the method of the present invention, and the thin line represents the structure of the substrate binding site of lysopath pepsin. The ASP79 is 79
Position means aspartic acid, and ASP218 means aspartic acid at position 218.

A first embodiment of the present invention will be described with reference to the flow charts of FIGS. Figure 6 shows
The flow from inputting the coordinates of a known ligand molecule to obtaining three-dimensional lattice point information by the PS method is shown in FIG.
And 5 show the flow from inputting the atomic coordinates of the ligand molecule and the three-dimensional lattice point information obtained by the RECEPS method by the LINKOR method to outputting the molecular structure of the novel ligand. In addition, in FIGS. 4-6, R and L show each step.

First, in R1 of FIG. 6, the atomic coordinates of one kind of ligand molecule known to have physiological activity, or two or more kinds of ligand molecules known to have similar physiological activity are input. To do. As the structure of this ligand molecule, a structure determined by crystal analysis, a similar structure in a crystal database, or a structure obtained by molecular modeling using energy calculation can be used.

Next, at R2, for each ligand molecule, the charge of each atom is calculated by the molecular orbital method calculation,
Further, the hydrogen-bonding functional group is given a type number for each functional group. Here, the hydrogen-bonding functional group means a functional group containing hydrogen for forming a hydrogen bond or a hetero atom having a lone atom pair.

Next, in R3, it is determined whether or not there is one kind of ligand molecule. When the number of ligand molecules is one, the step of R11 is performed without performing the steps of R4 to R10 described below. When there are two or more types of ligand molecules in R3, two types of molecules are selected from the ligand molecules in R4, and one is used as a template molecule and the other is used as a trial molecule.

Next, at R5, it is selected whether the ligand molecules are automatically superposed or interactively superposed. Here, superposition of molecules means placing three-dimensional structures of a plurality of active molecules in corresponding orientations in the same space in order to three-dimensionally search and compare homology and differences in molecular structures and properties. Say. What properties and physical quantities should be focused on (shape of surface of molecule, position of contained atoms,
The problem is how to evaluate the goodness of overlap, such as physical and chemical properties. For example, in RECEPS, it is possible to perform superimposition in which importance is attached to the matching of submolecular properties such as hydrogen bond, ionic bond, and hydrophobic interaction for interacting with the receptor. Molecular superposition may be performed using a molecular model, but it is easy and quantifiable.
It is preferable to use computer graphics because the coordinates can be stored as they are. In addition, automatic superposition of molecules refers to a method in which a computer automatically finds a superposition method while covering the positional relationship and molecular conformation of superposition. For example, in RECEPS, a special least squares calculation is performed so that the hydrogen-bonding atoms on the acceptor side coincide with each other assuming that the same receptor is bound to the same site. Further, the interactive superposition of molecules refers to superimposing the molecules while rotating, translating, or binding rotating the molecules while referring to the index of overlap on a computer graphics display.

In the step of R5, it is generally preferable to select the automatic superposition, but when there are few hydrogen bonding sites in the molecule and it is difficult to use the automatic superposition method, the interactive superposition is performed. Good to choose. R5
When the automatic superimposition of ligand molecules is selected in, next, in R6, automatic superimposition using a dummy atom is performed. A dummy atom is based on the position of the group (eg, hydrogen donor group) involved in the interaction of one molecule when there are two molecules (eg, receptor and ligand) forming a hydrogen bond. , A virtual atom arranged at a position which is presumed to be appropriate as a position of a group (for example, hydrogen accepting group) involved in the interaction of the other molecule. For example, in a receptor-ligand system in which two or more hydrogen bonds are presumed to be involved in the activity of the ligand, they are arranged on the receptor side based on the position and nature of the hydrogen-bonding functional group of the template molecule. The mutual relationship between the template molecule and the trial molecule and the template molecule should be adjusted so that the dummy atom matches the dummy atom located on the acceptor side to the maximum extent based on the position and nature of the hydrogen-bonding functional group of the trial molecule. A model in which the template molecule and the trial molecule are superposed can be created while changing the conformation of the trial molecule. All ligand molecules are superposed by repeating the automatic superposition with the template molecule by replacing the trial molecule (Y.Kat
o, A. Inoue, M. Yamada, N. Tomioka, and A. Itai, Compu
ter-Aided Molecular Design 6, pp.475-486 (1992))
.

When interactive superposition is selected in R5, next, in R7, a region for creating a three-dimensional lattice point is set for the template molecule. Next, in R8, three-dimensional lattice point information (shape, hydrogen bonding, electrostatic potential, aromaticity, etc.) about the template molecule is calculated and stored. Next, at R9, the trial molecule is interactively superposed on the template molecule while referring to the index for coincidence of physicochemical properties calculated in real time using the above-mentioned three-dimensional lattice point information. By repeating the superposition with the template molecule while changing the trial molecule, all the ligand molecules are superposed.

Next, in R10, an automatic superposition model of the template molecule and the trial molecule obtained in R6, or R9
Optimize the interactive superposition model of the template molecule and the trial molecule obtained in. All of the superposition models with good superposition indexes obtained by R6 or R9 were re-evaluated by the indexes (hydrogen bonding, electrostatic potential, shape, aromaticity, etc.) using three-dimensional lattice points, and Get a promising overlay model.

Alternatively, by using the result of superposition obtained at R6 or R9 as an initial structure, the molecular structure is interactively manipulated to improve the superposition model, or superposition is performed by the Simplex method using three-dimensional lattice point data. By optimizing the registration model, an appropriate registration model is obtained. next,
In R11, a region for creating a three-dimensional lattice point is set based on the overlapping structure of the ligand molecules obtained in the steps of R2 to R10 or the structure of the single ligand molecule input in R1.

Next, at R12, three-dimensional lattice point information for all molecules is calculated within the region set at R11. Receptor mapping can be performed based on this three-dimensional lattice point information. Here, the receptor mapping means to estimate and express the environment of the receptor from the information of the ligand molecule when there is no experimental information about the three-dimensional structure of the receptor. Receptor mapping by RECEPS uses three-dimensional lattice points inside and around the molecule, and based on the structure of a ligand molecule or a plurality of ligand molecules superposed on each other, the size and shape of the inner pore of a receptor (receptor) model, Expected sites of hydrogen bonding functional groups, electrostatic properties, aromaticity, etc. are expressed. The space occupied by the three-dimensional lattice points occupied by one or more molecules is assumed to be the inner pore of the receptor. As for the electrostatic potential in the area outside of that, an average value weighted by activity at each three-dimensional lattice point is adopted.

Next, at R13, a hydrogen bonding site is set. When there are multiple ligand molecules, a hydrogen-bonding functional group with a high degree of commonality between the superposed molecules is set as the hydrogen-bonding site, and when there is only one kind of ligand molecule, it may be important for the user to judge. A hydrogen-bonding functional group is set as a hydrogen-bonding site.

Next, at R14, the three-dimensional lattice point information is output to a file. Next, at R15, the atomic coordinates of the superposition model of the ligand molecules are output. Next, in L1 of FIG. 4, the atomic coordinates of the known single ligand molecule or the atomic coordinates of the superposition model of the ligand molecules output in R15 are input.

Next, in L2, the charge of each atom is calculated in advance by the molecular orbital method calculation for each ligand molecule, and for the hydrogen bonding functional group, the type number of each functional group is determined by the user. Give it. Next, in L3, the three-dimensional lattice point information calculated in R12 is input. Next, at L4, a functional group presumed to be essential for activity is extracted from the above-mentioned known ligand molecule or ligand molecule group that interacts with the receptor.

Furthermore, a new ligand molecular structure can be constructed by preparing a plurality of functional groups having equivalent interactions as fragments of these functional groups and sequentially substituting them. Examples of the above-mentioned substitutable functional groups are shown in Table 1 below.

[0050]

[Table 1] Table 1 No. Functional group 1 SP ² N 2 SP ³ N (protonated) 3 SP ³ N 4 aromatic N (protonated) 5 aromatic N 6 hydroxy group O 7 ether O 8 carbonyl group O 9 O 10 phenyl group of carboxylate anion Next, at L5, the position and direction of the functional group extracted in the above step L4 are set.

When the ligand molecule is single, the position of the functional group in the molecule is used as the site, and when the ligand molecule is a plurality of molecules, the corresponding functional groups in the respective molecules subjected to molecular superposition are With the position of the center of gravity as the site,
By setting the fragment structure coordinates of each functional group, the position and direction of the extracted functional group are specified. If there are other positions and directions that are expected to have the same effect, they can be sequentially replaced.

Next, in L6, the distance between the sites is calculated. Next, at L7, the site connection method is set. When there are two sites, only the route connecting them needs to be considered, but when there are three or more sites, the generated structure differs depending on which site is connected and in what order. It is possible to select from three methods of connecting linearly, connecting all sites with a core at the center, and connecting all sites in a ring. Although it can be set so as to cover all connection methods, it is usually preferable to select a linear connection method.

For example, if there are three sites A, B, and C, A-B-C, A-C-B, C-A-B
There are 6 ways of linear connection. These can be tried one after another, but normally it is preferable to perform only one way in which the sites are connected in ascending order of distance. Also, when the number of sites is large, it is possible to specify that some of them are connected without connecting all of them.

Next, in L8, 1 of how to connect sites
Choose one. For example, the connection method of ABC is selected. Next, at L9, the number of bonds between sites is set. For example, when the connection method of A-B-C is selected, the number of inter-site bonds is two, A-B and B-C.

Next, in L10, two sites to be combined are set. For example, select two sites A and B. Next, in L11, the upper limit and the lower limit of the number of atoms involved in the bond between the sites (hereinafter, referred to as “bonded atom number”) are set. For example, when two sites A and B are selected, the appropriate number of atoms involved in the bond between AB can be calculated from the distance between A and B according to the following formula.

Lower bound number of atoms = rounded down to the right of decimal point {(A
-Minimum distance between B) / (2.735 / 2)}-1 Maximum number of bonded atoms = Round up after decimal point {(Minimum distance between A-B) / (2.006 / 2)} The constant 2.735 in the above formula is- C1≡C2-C3≡
Is the distance between C1 and C3, and the constant 2.006 is −
C1 = C2-C3 = is the distance between C1 and C3.

Next, in L12, the number of bond atoms is set. For example, in the above calculation, when the upper limit of the number of bonding atoms is 5 atoms and the lower limit thereof is 2 atoms, first, a bond path connecting the sites with 2 atoms, which is the lower limit number of bonding atoms, is searched, and then 3 The number of bonding atoms is sequentially increased, such as searching for a bonding path that bonds the sites with atoms, and the maximum number of bonding atoms, 5 atoms, is searched.

Next, at L13, the bond atom species is set. As the bonding atom species, the combination of probe atoms shown in Table 2 can be prepared and used sequentially,
If necessary, it is possible to limit to only carbon atoms or to use fragments such as amide and benzene ring.

[0059]

Type [Table 2] Table 2 Probe atom ^{C: SP 3 1 C: SP} 2 2 C: group 3 C: Aromatic ^{49 # 1N: SP 2 9 #} 2N: SP 3 ( protonated) 39 # 3N: SP ³ 8 # 4N: SP ² (aromatic / protonated) 9 (50) # 5N: SP ² (aromatic) 9 (50) # 6O: hydroxy group 6 # 7O: ether group 6 # 8O: carbonyl group 7 # . 9O: carboxylate anion 47 # 10C: phenyl group 51 H: bound to C: SP ² 5 H: bound to C: SP ³ 5 H: N binding: SP ³ 28 H: bonded to C: aromatic 5 H: Bonded to O: hydroxy group 21 Next, at L14, based on a bond distance and a bond angle with an atom (hereinafter, referred to as a “key atom”) in a site that bonds with the probe atom or another probe atom, Territories that can exist Set the area roughly (see Figure 2).

That is, in the bonding method 1, the upper and lower limits of the address of the three-dimensional lattice point where the bonding atom can exist are calculated. Further, in the bonding method 2, a circle in which a bonding atom can exist is calculated. Then, at L15,
A probe atom is arranged in the region set by L14.
In the combining method 1, one point of the three-dimensional lattice points existing in the region set by L14, and in the combining method 2,
Probe atoms are generated at regular intervals on the circumference.

Next, at L16, an appropriate one is selected from the probe atoms. Whether or not the probe atom is in the inner hole of the receptor is judged by the lattice point information of the closest three-dimensional lattice point, and the one in the spatial region in the inner hole of the receptor is selected. Furthermore, it is determined whether the selected probe atom has a bond distance, a bond angle, or a twist angle with a key atom in the site or another probe atom within a certain allowable range from an ideal value (standard value), If it is within this certain range, the three-dimensional lattice point or the point on the circumference is adopted as the position of the bonding atom.

Next, at L17, it is judged whether all three-dimensional lattice points or points on the circumference within the area set at L14 have been selected. When all three-dimensional lattice points or points on the circumference within the area set by L14 have not been selected, the process returns to L15. The steps L15 to L16 are repeated for all three-dimensional lattice points or points on the circumference in the region where the probe atom can exist, and all adopted three-dimensional lattice points or points on the circumference are registered. .

Next, in L18, it is determined whether or not all of the bond atom species prepared in L13 have been selected. When all are not selected, the process returns to L13, the bond atom species is changed, and the steps of L14 to L17 are repeated. Next, in L19, it is determined whether or not all the bonding atom numbers are selected in L12. When all the bond atom numbers are not selected, the process returns to L12, the bond atom number is changed, and the steps of L13 to L18 are repeated.

Next, at L20 of FIG. 5, a bond path between the sites is generated. For example, by combining method 1, a
When the site A and the site B are connected by two atoms of b and b, the set a of the three-dimensional lattice points registered for the site A
Set b of 3D grid points registered for ¹ and site B
^From all combinations with ¹ , select only the combination with the appropriate bond distance, bond angle, and twist angle to complete the bond path.

Further, according to the coupling method 1, a, b and c
In the case of connecting site A and site B with the three atoms of the above, for each ^one of the three-dimensional lattice points of the set of three-dimensional lattice points a ¹ adopted as described above as the position of the atom bonded to the site A , L14 to L17, a
Obtain a set c of three-dimensional lattice points adopted as the positions of atoms that bond to ¹ . Three-dimensional lattice points included in c and site B
Bond distance from among all combinations with the set b ¹ of three-dimensional lattice points registered as the position of the atom bonded to
Only bond angles and combinations with a suitable twist angle are selected to complete the bond path.

The same applies when the sites A and B are connected by four or more atoms. For example, when the site A and the site B are connected by 2n atoms, a set of three-dimensional lattice points from the site A side. after the obtained from a ¹ in order to a ^n, a set of three-dimensional grid points from the site B side from b ¹ to b ⁿ in order, a ⁿ
Bond distances of -b ⁿ , a ^n-1 -a ⁿ -b ⁿ and a ⁿ -b
bond angle of ⁿ -b ^n-1 is employed only as a coupling path reasonable.

In addition, for example, when the site A and the site B are connected by two atoms of a and b by the bonding method 2,
Should be on the circumference of the circle (a) that is inclined by the angle corresponding to the atomic species of A and keeps the bond distance between Aa. All points on the circumference of circle (a) are candidates for the position of a, as long as they do not overlap with the region where the receptor exists, and probe atoms are placed at points taken on this circumference every 5 to 10 °. I will put it down. The same applies to b bound to the site B. Only those combinations in which the distance between a and b and the angle between A and A and B and A and B are appropriate are selected to complete the binding pathway.

When the site A and the site B are connected by three atoms of a, b and c by the bonding method 2, the circle (a) and the circle are
In the same way that (b) was calculated, from one point a on the circle (a), the angle A−a−c and the distance a−c are appropriate for the atomic species of atoms a and c. Circle in which c can exist (c)
Is calculated. The probe atom c on the circle (c) and the probe atom b on the circle (b) have reasonable distances c-b and a-c-
If it is possible to have an angle of b and an angle of c-b-B,
It is registered as a connection route between A and B. The same applies when connecting the sites A and B with four or more atoms.

Next, at L21, least squares superposition between the coupling paths is performed, and those having a least square residual less than a certain value are removed as similar structures. Since many joint paths searched as described above are searched using three-dimensional lattice points or points with a constant interval on the circumference, those essentially belonging to the same structure are registered as different paths. It can happen. Therefore, the first binding pathway obtained from the above process is used as a template for judging the similarity between binding pathways, and the binding pathways obtained after the second are sequentially superposed by least squares superposition, Those with squared residuals below a certain value are removed, and those with a squared difference above a certain value are registered as templates to create template groups. The binding pathways that make up this template group are dissimilar to each other.

Next, in L22, it is determined whether or not all the two sites to be combined have been selected in L10. If all are not selected, the process returns to L10, another site pair is set, the steps of L11 to L21 are repeated, and the adopted coupling route is registered. Then L2
In 3, a new ligand molecule scaffold is formed by combining all binding pathways between each site.

Next, in L24, it is determined whether or not all the site connection methods have been selected in L8. If all of the site connection methods have not been selected, return to L8, select another order for connecting sites (for example, A-C-B), and select L
Repeat steps 9-L23. Next, in L25, it is determined whether or not the designation of the position and direction of the functional group performed in L5 is changed to another position and direction where the same effect is expected, without changing the interaction site on the receptor side. When changing the position and direction of the functional group, return to L5 and specify the position and direction of the functional group set in L5 without changing the interaction site on the receptor side. And the steps of L6 to L24 are repeated. For example, L1
If you input the atomic coordinates of multiple ligand molecules with,
You may specify the position and direction of the functional group of each ligand molecule.

Next, at L26, it is determined whether or not the operation for changing the kind of the functional group extracted at L4 to another functional group capable of interacting with the receptor is performed. When performing this operation, returning to L4, the type of the functional group extracted in L4 is changed to another functional group capable of interacting equivalent to the acceptor, and L5 to L25 are repeated. Next, at L27,
Output the entire ligand molecular scaffold constructed by the above steps.

Further, at L28, one of all ligand molecular skeletons is selected. Next, in L29,
Hydrogen atoms are added to atoms whose valences are not satisfied in the ligand molecular skeleton by calculating the bond distance and angle. If there are no atoms with unsatisfied valences, this step is omitted. Then, in L30, it is determined whether or not a ring structure needs to be formed in the molecular structure of the ligand under predetermined conditions, and if necessary, a ring structure is formed.

For example, when the distance between two hydrogen atoms is extremely close (0.6 angstrom), one carbon atom is placed at the center of these two atoms, and this carbon atom is replaced by each hydrogen atom described above. When the valence angle is within the allowable range when it is bonded to the atom that was bonded to, this carbon atom is adopted, and two hydrogen atoms are removed to form a ring structure ((a) in FIG. 3). See).

Next, at L31, a structure having a similar ring structure formed from another bonding pathway is removed. When a ring structure is formed in a ligand molecule as described above, it is possible that a different binding pathway essentially forms the same ring structure and is registered as a different binding pathway. The structure with a similar ring structure formed from is removed. This step can be performed in the same manner as in L21.

Next, in L32, the degree of freedom is restricted so that the position and direction of the functional group extracted in L4 are not changed, and the structure optimization calculation of the ligand molecule is performed to remove the molecular structure having very high energy. To do. Empirical energy calculations can be used to optimize the ligand molecular structure,
For example, the molecular force field calculation program MM2 (NL Alling
er, RA Kok and MRImam, J. Comp. Chem. 9 , 591
-595, (1987)) energy function and force field parameters can be used. The energy can be minimized by using a conjugate gradient method, and the functional group can be fixed by excluding the atom in the functional group set in L4 from the energy minimization parameter.

Furthermore, in L33, a portion where the ring structure is more stable due to interatomic contact including a hydrogen atom is searched for, and removal of atoms and removal of atoms are considered while considering bond length, bond angle, and twist angle. Forming a new ring structure by / or substitution (see (b) of Figure 3). This process is repeated until no new ring structure is formed. Then, at L34, the analogous structure formed from another binding pathway and ultimately settled in the same ring structure is removed.

This step can be carried out in the same manner as in L21. Next, at L35, the obtained ligand molecular structures are narrowed down according to predetermined conditions. In the case of a rigid structure in which the molecular structure of the obtained ligand does not have a rotatable single bond, unconstrained structure optimization is performed,
It is possible to remove the initially designated functional groups whose positions or directions are different from each other. Alternatively, both unconstrained and constrained structure optimization calculations may be performed, and those having a large energy difference above a certain level may be removed.

If the molecular structure of the obtained ligand is not a rigid structure, constrained structure optimization calculation can be performed to remove those whose functional groups extracted in L4 are displaced from each other in position or direction. it can. Next, at L36,
The atomic coordinates of the structure of the obtained ligand molecule are output. Next, in L37, it is determined whether or not all ligand molecule skeletons have been selected in L28. If all the ligand molecule skeletons have not been selected, the process returns to L28, the next ligand molecule skeleton is selected, and steps L29 to L36 are repeated.

The method of the present invention was applied to morphine, which has no conformational freedom and is known to have a functional group essential for activity. Morphine is a natural compound isolated from poppy flowers that exhibits a strong analgesic effect, and a number of related compounds have been designed based on its structure and chemically synthesized to investigate the analgesic activity. The effectiveness of the method of the invention is demonstrated if the molecular structures of those known analgesic active compounds are constructed by the method of the invention.

The chemical structure of morphine is shown in FIG. 8 (a), and the crystal structure of bromate is shown in FIG. 8 (b). As a result of various modifications of the molecular structure and investigation of the activity, it is found that the benzene ring and the nitrogen atom are essential for the activity in the molecular structure, and that both of them have a specific positional relationship in morphine. It turned out to be important. It is not clearly known what state of this nitrogen is essential, but assuming that the protonated state of the tertiary amine is active, the direction of H bound to N in the morphine crystal is changed to the direction of the lone electron pair. Assuming that the positions of the constituent atoms of the benzene ring do not matter as long as the positions of the ring currents of the π electrons match, the position of the center and the direction of the normal vector are assumed to be essential for the activity of the ligand molecule The position and direction of the functional group to be generated are specified (Fig. 8
(C)). On the other hand, RECEPS is used to perform receptor mapping from a single molecule of morphine to construct a receptor model on a three-dimensional lattice point (see FIG. 9).
The molecular structure of the ligand was constructed by OR. The space between the three-dimensional lattice points was 0.35A. Table 3 shows the calculation conditions used.

[0082]

[Table 3]Table 3 Calculation conditions Description ARECEP = RECEPS Creates three-dimensional lattice point information from ligand molecules. GRDNAM = morph.crg File name of 3D lattice point information NUTMPM = 1 Number of molecules used as template ATMPNM = morph2.d Coordinate file of template molecules NFRAG = 2 Number of functional groups IFRAG = 1 Quaternary amine (functional group 1) Is the atom in the coordinate file. IFRAG = 38 What number atom in the coordinate file is the benzene ring atom (functional group 2)? LKORDER = 1 2 Connect functional groups 1 and 2. RSLMT = 0.12 If the least square residual is less than this, the structure is similar. ANGFIL = angl.parm Bond angle parameter file for structural optimization. DISFIL = dist.parm File of bond distance parameters for structural optimization. LNKDIS = 0.38 Allowable range from standard value of bond distance (unit: Angstrom) LNKANG = 6.5 Allowable range from standard value of bond angle (unit: °) LNKTOT = 8.0 Allowable range from standard value of twist angle (unit: °) RNGCON = 0.7 If 0.7 times or less of the sum of van der Waals radii, it is judged whether a ring structure can be formed. USRFLG = 1 10 Select only the phenyl group No. 10 in Table 1 as fragment 1. USRFLG = 2 2 Select only the quaternary amine of No. 2 in Table 1 as fragment 2. It

However, in the construction of the molecular structure of the ligand, in the step of L20, the binding route between the sites is generated by the binding method 1, the position and direction of the functional group are not reset in the step of L25, and No substitution to equivalent functional groups was made in the L26 step. Furthermore, L3
In step 5, the MNDO method in the semi-empirical molecular orbital calculation program MOPAC was used to perform optimization without restrictions, and those in which the positional relationship between the functional groups was largely changed were excluded. The ligand molecular structure was narrowed down. As a result, about 50 molecular structures were obtained. The molecular structure of part 1 is shown in FIG. These molecular structures include a large number of molecular skeletons of compounds that are known to exhibit activity equal to or higher than that of morphine. FIG. 11 shows the structures of known active compounds having those molecular skeletons. Therefore, it is highly possible that the other compounds and their derivatives exhibit analgesic activity equivalent to or higher than that of morphine.

The second embodiment of the present invention will be described below. When the structure of the receptor-ligand complex was elucidated, the molecular structure of the ligand could be constructed as follows. Instead of the steps of R1 to R15 and L1 to L4 of the first embodiment, the information of the three-dimensional lattice points created in the inner hole of the receptor is calculated based on the known structure of the receptor, and The same processing steps as in the first embodiment are performed, except that the functional group of the ligand molecule that directly interacts with the receptor is extracted and the structural coordinates of the functional group are set.

The above-described method was applied to the bacterial proteolytic enzyme lysopathpepsin and its peptide-like inhibitor (C-terminal) Pro-
Phe-His-Phe Ψ [CH ₂ NH] -Phe-Val-Tyr (N-terminal) (wherein Ψ [CH ₂ NH] is a peptide bond CONH- at this part is CH.
Indicates that it is ₂ NH. ) Was applied to. First, from the structure of the inhibitor in the enzyme-substrate complex crystal, five functional groups that directly interact with the substrate-binding site of the enzyme were extracted and fixed in that position (see FIG. 12). 5 above
It was designated to connect any three of the extracted functional groups. GREEN (Journal of Computer Ages Molec
ular Design, vol.1, pp.197-210 (1987), Nobuo Tomio
ka, Akiko Itai, and Youichi Iitaka) was used to represent the region that the center of the atom in the ligand molecule puts in as three-dimensional lattice point information. When the molecular structure of the novel ligand was constructed in this region, the molecular structure shown in FIG. 13 was obtained. These molecules are non-peptide,
As shown in FIG. 14, it can be stably arranged at the same position in the inner hole of lysopath pepsin as in the above peptide-like inhibitor. Furthermore, by calculating the binding strength of these molecules with the lysopas pepsin enzyme by energy calculation, it was found that they showed almost the same degree of interaction (complex stability) as the above peptide-like inhibitors. It was Therefore,
Compounds having these molecular structures and derivatives thereof,
It is highly likely that it has strong lysopath pepsin inhibitory activity.

The third embodiment of the present invention will be described below. When the three-dimensional structure of the receptor alone is elucidated and the environment of the drug binding site is known, R1 to R of the first embodiment are used.
15, and the information of the three-dimensional lattice points created in the inner hole of the receptor is calculated in place of the steps L1 to L4, and
The molecular structure of the ligand molecule is constructed by performing the same processing steps as in the first embodiment except that the user sets the types and coordinates of two or more functional groups that can interact with the functional groups present in the receptor. It is possible.

[Brief description of drawings]

FIG. 1 illustrates the concept of the method of the present invention.

FIG. 2 shows a method for coupling functional groups in the method of the present invention.

FIG. 3 shows a method for forming a ring structure in the present invention.

FIG. 4 shows a part of a flow chart of one embodiment of the method of the present invention using LINKOR.

FIG. 5 shows a part of a flow chart of one embodiment of the method of the present invention using LINKOR.

FIG. 6 shows a flowchart of a molecular superposition method using RECEPS and receptor mapping.

FIG. 7 shows a concept of a molecular superposition method using RECEPS and receptor mapping.

FIG. 8 shows the molecular structure of morphine, (a) the chemical structure of morphine molecule, (b) the crystal structure of morphine bromate molecule, and (c) the molecular structure of morphine. The position and direction of the extracted functional group are shown.

FIG. 9 shows a morphine receptor model expressed using three-dimensional lattice points. The space surrounded by the cage represented by the diagram in (a) shows the space assumed to be allowed by the ligand molecule. (B) further shows the position of the expected anionic or hydrogen-bonding heteroatom on the acceptor side.

FIG. 10 shows a part of the molecular structure of the ligand of the morphine receptor constructed by the method of the present invention.

FIG. 11 shows the molecular structure of a group of compounds known to have analgesic activity equivalent to that of morphine.

FIG. 12 shows the structures of inhibitors of lysopath pepsin.

FIG. 13 shows the molecular structure of the ligand of lysopath pepsin constructed by the method of the present invention.

FIG. 14 shows a state in which a ligand molecule having a molecular structure constructed by the method of the present invention is arranged in the inner pore of lysopath pepsin.

Claims (19)

[Claims] 1. A method for constructing a molecular structure of a ligand having a physiological activity, comprising: (i) extracting two or more functional groups presumed to be essential for the physiological activity of the ligand, and determining the position of the functional group. And the first step of specifying the direction, (ii) the first step
The second step of setting the connection method between the functional groups extracted in the step,
(iii) a third step of designating the number, type, and existence region of atoms connecting the two functional groups, (iv) arranging a probe atom in the inner hole of the receptor of the ligand, and determining the position of the probe atom. If a predetermined condition is satisfied, a fourth step is adopted as the position of the atom connecting the two functional groups, (v) By repeating the fourth step for all the atoms specified in the third step, 2 By repeating the third to fifth steps for the fifth step of creating a bonding path between the two functional groups, and (vi) for all combinations of the two functional groups set to be connected in the second step. The method as described above, which comprises the sixth step of forming a skeleton of the ligand molecule by combining the obtained binding pathways. 2. The method for constructing the molecular structure of a physiologically active ligand according to claim 1, wherein the fourth step is performed by arranging probe atoms on a three-dimensional lattice point. 3. The physiological activity according to claim 1, wherein the fourth step is carried out by arranging probe atoms at points on the circumference where bond atoms can be present, which are calculated from bond distances and bond angles. A method of constructing a molecular structure of a ligand. 4. A method for constructing a molecular structure of a ligand having physiological activity, comprising: (i) obtaining three-dimensional lattice point information based on the molecular structures of one or more known ligands, First step of constructing a model of inner pore, (ii) extracting two or more functional groups presumed to be essential for physiological activity from the molecular structure of the known ligand, and the position and direction of the functional groups The second step of specifying (iii)
A third step of setting the way of connecting the functional groups extracted in the second step, (iv) a fourth step of specifying the number, type and existence region of atoms connecting the two functional groups, (v) the acceptance A fifth step of arranging a probe atom in the inner pore of the body and adopting it as a position of an atom connecting two functional groups when the position of the probe atom satisfies a predetermined condition, (vi) the fourth step Repeating the fifth step for all the atoms specified in Step 6 to create a bond path between the two functional groups.
Step, and (vii) For all combinations of the two functional groups set to be connected in the third step, the binding pathways obtained by repeating the fourth step to the sixth step are combined to combine the ligand A method as described above, comprising the seventh step of forming a molecular backbone. 5. A method for constructing a molecular structure of a ligand having physiological activity, comprising: (i) obtaining three-dimensional lattice point information based on the molecular structures of one or more known ligands, First step of constructing a model of inner pore, (ii) extracting two or more functional groups presumed to be essential for physiological activity from the molecular structure of the known ligand, and the position and direction of the functional groups The second step of specifying (iii)
A third step of setting the way of connecting the functional groups extracted in the second step, (iv) a fourth step of specifying the number, type and existence region of atoms connecting the two functional groups, (v) the acceptance A fifth step of arranging a probe atom in the inner pore of the body and adopting it as a position of an atom connecting two functional groups when the position of the probe atom satisfies a predetermined condition, (vi) the fourth step Repeating the fifth step for all the atoms specified in Step 6 to create a bond path between the two functional groups.
Step (vii) For all combinations of the two functional groups set to connect in the third step, the fourth step to the sixth step
A seventh step of forming a skeleton of the ligand molecule by combining the binding pathways obtained by repeating the steps, (viii) whether or not there is an atom whose valence is not satisfied in the molecular skeleton of the ligand. Determine whether
If the atom is present, the eighth step of adding a hydrogen atom to the atom, (ix) by predetermined conditions, to determine whether to form a ring structure in the molecular structure of the ligand, The above method, which comprises a ninth step of forming a ring structure if necessary, and (x) a tenth step of optimizing the molecular structure of the ligand. 6. Further, the positions and directions of the functional groups specified in the second step are sequentially specified again in the positions and directions which are estimated to have the same effect, and the third step to the tenth step are carried out. A method for constructing a molecular structure of a physiologically active ligand according to claim 5, which is repeated. 7. The method according to claim 5, wherein the functional groups extracted in the second step are sequentially replaced with other functional groups having equivalent physicochemical properties, and the third to tenth steps are repeated. A method for constructing a molecular structure of a ligand having physiological activity. 8. A method for constructing a molecular structure of a physiologically active ligand, comprising: (i) information on a three-dimensional lattice point created in the inner pore of the receptor based on the known receptor structure of the ligand. (Ii) a second step of extracting two or more functional groups that interact with the receptor from a functional group in a known ligand molecule and designating the position and direction of the functional group; iii) a third step of setting the connection method between the functional groups extracted in the second step, (iv) the number of atoms connecting the two functional groups,
Fourth step of designating type and existence region, (v) Placing a probe atom in the inner hole of the receptor and connecting two functional groups when the position of the probe atom satisfies a predetermined condition The fifth step adopted as the position of the atom, (vi) the fourth step
The sixth step of creating a bond path between two functional groups by repeating the fifth step for all the atoms specified in the step, and (vii) the two functional groups set to be connected in the third step. The method as described above, which comprises the seventh step of forming the skeleton of the ligand molecule by combining the binding pathways obtained by repeating the fourth to sixth steps for all combinations of groups. 9. A method for constructing a molecular structure of a physiologically active ligand, comprising: (i) information on a three-dimensional lattice point created in the inner pore of the receptor based on the known receptor structure of the ligand. (Ii) a second step of extracting two or more functional groups that interact with the receptor from a functional group in a known ligand molecule and designating the position and direction of the functional group; iii) a third step of setting the connection method between the functional groups extracted in the second step, (iv) the number of atoms connecting the two functional groups,
Fourth step of designating type and existence region, (v) Placing a probe atom in the inner hole of the receptor and connecting two functional groups when the position of the probe atom satisfies a predetermined condition The fifth step adopted as the position of the atom, (vi) the fourth step
A sixth step of creating a bond route between two functional groups by repeating the fifth step for all atoms specified in the step, (vii) two functional groups set to be connected in the third step. For all combinations of
The seventh step of forming a skeleton of the ligand molecule by combining the binding pathways obtained by repeating the steps to the sixth step, (viii) an atom whose valence is not satisfied is present in the molecular skeleton of the ligand. It is judged whether or not it exists, and if the atom is present, the eighth step of adding a hydrogen atom to the atom, (ix) it is necessary to form a ring structure in the molecular structure of the ligand according to predetermined conditions. The method as described above, including the step 9 of determining whether or not there is any, and forming a ring structure if necessary, and (x) the step 10 of optimizing the molecular structure of the ligand. 10. Further, the positions and directions of the functional groups specified in the second step are sequentially specified again in the positions and directions which are presumed to have an equivalent effect, and the third to tenth steps are carried out. A method for constructing a molecular structure of a bioactive ligand according to claim 9, which is repeated. 11. The method according to claim 9, wherein the functional group extracted in the second step is sequentially replaced with another functional group having an equivalent physicochemical property, and the third step to the tenth step are repeated. A method for constructing a molecular structure of a ligand having the described physiological activity. 12. A method for constructing a molecular structure of a physiologically active ligand, comprising: (i) information on a three-dimensional lattice point created in the inner pore of the receptor based on the known receptor structure of the ligand. Step (ii), selecting two or more functional groups capable of interacting with the receptor and designating the position and direction of the functional groups, (iii) selecting in the second step Third step of setting the way of connecting the functional groups, (iv) Fourth step of specifying the number, type and existence region of atoms connecting the two functional groups, (v) Probe in the inner pore of the receptor If the atoms are arranged and the positions of the probe atoms satisfy a predetermined condition, the fifth step is adopted as the positions of the atoms connecting the two functional groups, (vi) for all the atoms specified in the fourth step. , Creating a bond pathway between two functional groups by repeating the fifth step Sixth step, and (vii)
The skeleton of the ligand molecule is formed by combining the binding pathways obtained by repeating the fourth step to the sixth step for all combinations of the two functional groups set to be connected in the third step. The above method comprising a seventh step. 13. A method for constructing a molecular structure of a physiologically active ligand, comprising: (i) information on a three-dimensional lattice point created in the inner pore of the receptor based on the known receptor structure of the ligand. Step (ii), selecting two or more functional groups capable of interacting with the receptor and designating the position and direction of the functional groups, (iii) selecting in the second step Third step of setting the way of connecting the functional groups, (iv) Fourth step of specifying the number, type and existence region of atoms connecting the two functional groups, (v) Probe in the inner pore of the receptor If the atoms are arranged and the positions of the probe atoms satisfy a predetermined condition, the fifth step is adopted as the positions of the atoms connecting the two functional groups, (vi) for all the atoms specified in the fourth step. , Creating a bond pathway between two functional groups by repeating the fifth step Sixth step, by combining (vii) the third for all combinations of the two functional groups configured to connect in step, the fourth step to the coupling path obtained by repeating the sixth step,
A seventh step of forming a skeleton of the ligand molecule, (viii)
The eighth step of determining whether or not there is an atom whose valence is not satisfied in the molecular skeleton of the ligand, and adding a hydrogen atom to the atom if the atom is present, (ix) predetermined Based on the conditions of step 9, it is judged whether or not a ring structure needs to be formed in the molecular structure of the ligand, and if necessary, a ninth step of forming a ring structure, and (x) the molecular structure of the ligand is optimized. The method as described above, comprising the step of: 14. Further, the positions and directions of the functional groups specified in the second step are sequentially specified again in positions and directions which are estimated to have the same effect, and the third step to the tenth step are performed. The method for constructing a molecular structure of a bioactive ligand according to claim 13, which is repeated. 15. The functional group extracted in the second step is further substituted with another functional group having an equivalent physicochemical property, and the third to tenth steps are repeated. A method for constructing a molecular structure of a ligand having the described physiological activity. 16. A method for constructing a molecular structure of a physiologically active ligand, comprising: (i) the atomic coordinates of one or more known ligand molecules and a three-dimensional lattice created within the inner pores of the receptor for said ligand. The first step of inputting point information and
(ii) a second step of extracting two or more functional groups presumed to be essential for physiological activity from the structure of the known ligand molecule, and designating the position and direction of the functional groups; (iii) Second
A third step of setting the connection method between the functional groups extracted in the step,
(iv) a fourth step of designating the number, type, and existence region of atoms connecting two functional groups, (v) arranging a probe atom in the inner hole of the receptor, and positioning the probe atom at a predetermined position. If the condition is satisfied, a fifth step is adopted as the position of the atom connecting the two functional groups, and (vi) the fifth step is repeated for all the atoms specified in the fourth step to obtain two functional groups. A sixth step of creating a bonding route between groups, and (vii) obtained by repeating the fourth to sixth steps for all combinations of the two functional groups set to connect in the third step The method as described above, comprising the seventh step of forming a scaffold of the ligand molecule by combining different binding pathways. 17. A method for constructing a molecular structure of a physiologically active ligand, comprising: (i) the atomic coordinates of one or more known ligand molecules and a three-dimensional lattice created within the inner pores of the receptor for said ligand. The first step of inputting point information and
(ii) a second step of extracting two or more functional groups presumed to be essential for physiological activity from the structure of the known ligand molecule, and designating the position and direction of the functional groups; (iii) Second
A third step of setting the connection method between the functional groups extracted in the step,
(iv) a fourth step of designating the number, type, and existence region of atoms connecting two functional groups, (v) arranging a probe atom in the inner hole of the receptor, and positioning the probe atom at a predetermined position. If the conditions are satisfied, a fifth step is adopted as the position of the atom connecting the two functional groups, and (vi) the fifth step is repeated for all the atoms specified in the fourth step to obtain two functional groups. The sixth step of creating a bond pathway between groups, (v
ii) For all combinations of the two functional groups set to be connected in the third step, the skeleton of the ligand molecule is formed by combining the binding pathways obtained by repeating the fourth to sixth steps. 7th step of forming, (viii) it is determined whether or not there is an atom whose valence is not satisfied in the molecular skeleton of the ligand, and if the atom is present, a hydrogen atom is added to the atom. 8th step, (ix) it is determined whether or not a ring structure needs to be formed in the molecular structure of the ligand based on predetermined conditions, and if necessary, a 9th step of forming a ring structure, and ( x) The method as described above, which includes the step 10 of optimizing the molecular structure of the ligand. 18. Further, the positions and directions of the functional groups specified in the second step are sequentially specified again in the positions and directions which are estimated to have the same effect, and the third step to the tenth step are performed. A method of constructing a molecular structure of a ligand having a physiological activity according to claim 17, which is repeated. 19. The method according to claim 17, wherein the functional groups extracted in the second step are sequentially replaced with other functional groups having equivalent physicochemical properties, and the third to tenth steps are repeated. A method for constructing a molecular structure of a ligand having the described physiological activity.