Patent Publication Number: US-2005143926-A1

Title: Method and apparatus for generating biologically-active-substance candidate structure, and computer product

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS  
      This application is based upon and claims the benefit of priority from the prior Japanese Patent Application No.2003-429177, filed on Dec. 25, 2003, the entire contents of which are incorporated herein by reference.  
     BACKGROUND OF THE INVENTION  
      1) Field of the Invention  
      The present invention relates to a method and an apparatus for generating biologically-active-substance candidate structure and a computer product for generating a structure of a novel biologically-active-substance candidate based on a protein form, such as medical, pharmaceutical, or agricultural product.  
      2) Description of the Related Art  
      Conventional methods of generating a candidate compound are roughly classified as follows. A first method is to design a scaffold based on common element extraction by superposing known drug molecules. A second method is to obtain bonding energies of large quantities of compounds in a library with a protein, respectively by a molecular dynamics calculation or the like, and screening candidates that are possibly bonded with the protein (a screening method by a docking simulation). A third method is to obtain a scaffold by selecting some partial structures that may match to a protein-side amino acid, and bonding the selected partial structures using a spacer (see, for example, Japanese Patent Application Laid-Open No. H7-133233). A fourth method is to pack pseudo atoms into an active site, and finding a possible scaffold structure from a most closely packed site (see, for example, Japanese Patent Application Laid-Open No. 2000-178209 Publication).  
      However, the conventional methods have following problems. Regarding the first method, the designed structure is limited to a less-novel structure similar to a well-known structure. In the second method, accurate obtaining of the bonding energies at a high speed is not always established, so that proper candidates cannot be selected. With the third method, although much candidate structure generation software adopts this method, an important element for candidate structures of “complementarity with a form of the protein active site” tends to be disadvantageously overlooked. The fourth method is the most highly evaluated method in terms of not missing possible candidates. However, the scaffold structure obtained by bonding packed pseudo atomic spheres is estimated to contain stereochemically large distortion, and candidate structures, which are eventually difficult to synthesize, may possibly be included in the candidates.  
     SUMMARY OF THE INVENTION  
      It is an object of the present invention to solve at least the above problems in the conventional technology.  
      The apparatus for generating a biologically-active-substance candidate structure according to one aspect of the present invention includes a first unit that selects fragments of an arbitrary compound, a second unit that stably locates the fragments selected, and a third unit that inputs pseudo monoatoms into the active site in which the arbitrary fragments are stably located, and constructs a molecular scaffold by bonding the fragments together, bonding the fragment with the monoatom, and bonding the monoatoms together.  
      The method of generating a biologically-active-substance candidate structure according to another aspect of the present invention includes selecting fragments of an arbitrary compound, locating stably the fragments selected, and inputting pseudo monoatoms into the active site in which the arbitrary fragments are stably located and constructing a molecular scaffold by bonding the fragments together, bonding the fragment with the monoatom, and bonding the monoatoms together.  
      The computer readable recording medium according to another aspect of the present invention stores a computer program that realizes the method according to the above aspect on a computer.  
      The other objects, features, and advantages of the present invention are specifically set forth in or will become apparent from the following detailed description of the invention when read in conjunction with the accompanying drawings.  
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
       FIG. 1  is a schematic for explaining an outline of a biologically-active-substance candidate structure generation method according to an embodiment of the present invention;  
       FIG. 2  is a flowchart of a process procedure for the biologically-active-substance candidate structure generation method according to the embodiment;  
       FIG. 3  is a schematic for illustrating an example of a hardware configuration of a biologically-active-substance candidate structure generating apparatus according to the embodiment;  
       FIG. 4  is a schematic for illustrating a functional configuration of the biologically-active-substance candidate structure generating apparatus according to the embodiment;  
       FIG. 5  is a flowchart of a process procedure for a fragment selecting processing according to the embodiment;  
       FIG. 6  is a flowchart of a process procedure for an MD calculation processing according to the embodiment;  
       FIG. 7  is a flowchart of a process procedure for monoatoms locating, binding probability estimation, and molecular scaffold construction processing according to the embodiment;  
       FIG. 8  is a table of conditions for determining pseudo atom locations according to the embodiment;  
       FIG. 9  is a schematic for illustrating a content of the condition ( 5 ) in the table shown in  FIG. 8 ;  
       FIG. 10  is a flowchart of a process procedure for the heteroatom substituent candidate selection, hetero atom substitution estimation, and determination processing according to the embodiment;  
       FIG. 11A  is a schematic for illustrating a state of a measured location on x-y plane;  
       FIG. 11B  is a schematic for illustrating a state of a measured location on x-z plane;  
       FIG. 12A  is a schematic for illustrating a state of a packing result on x-y plane;  
       FIG. 12B  is a schematic for illustrating a state of a packing result on x-z plane;  
       FIG. 13  is a schematic for explaining an example of a known inhibitor structure;  
       FIG. 14  is a schematic for explaining first example of a candidate ligand structure;  
       FIG. 15  is a schematic for explaining second example of the candidate ligand structure;  
       FIG. 16  is a schematic for explaining third example of the candidate ligand structure;  
       FIG. 17  is a schematic of a three-dimensional structure of the known inhibitor shown in  FIG. 13 ; and  
       FIG. 18  is a schematic of a three-dimensional structure of the candidate ligand shown in  FIG. 14 . 
    
    
     DETAILED DESCRIPTION  
      Exemplary embodiments of a method and an apparatus for generating a biologically-active-substance candidate structure, and a computer product according to the present invention will be explained below in detail with reference to the accompanying drawings.  
       FIG. 1  is a schematic for explaining an outline of a biologically-active-substance candidate structure generation method according to an embodiment of the present invention.  
      Several partial structures, which can be synthesized and are often applied as drugs, are first selected, and located in an active site of a protein. Thereafter, small partial structures or monoatoms are located therein so as to provide an overall location which is energetically stable. A molecular dynamics calculation is used for location searches. As the molecular dynamics calculation, a molecular dynamics (MD) method, a Monte Carlo (MC) method, or the like can be used. It is considered that the MD method is the most efficient method.  
      While searching the location at which the partial structures satisfactorily interact with the protein active site and at which the partial structures can be satisfactorily bonded together, the respective partial structures and monoatoms are coupled to thereby obtain a candidate structure. Thus, the candidate structure which has both novelty and synchronization probability can be generated.  
      Specifically, as shown in  FIG. 1 , a reference sign  101  denotes a compound fragment library,  102  denotes the active site,  103  denotes a candidate ligand structure of a candidate ligand compound (e.g., an inhibitor), and  111  to  115  denote compound fragments, respectively.  
      The compound fragments  111  to  115  in the fragment library  101  are input into the active site  102 , thereby performing initial packing (at S 150 ). Thereafter, using a field of force in which atoms repel each other when they are energetically close and attract each other when they are away, the active site  102  is subjected to so-called shaking to stabilize the compound fragments  111  to  115  packed into the active site  102  (at S 160 ). Further, at the obtained stable location of the compound fragments  111  to  115 , monoatoms are packed into the active site  102 , thereby bonding the fragments together (at a step S 170 ). As a result, the candidate ligand structure  103  is output.  
       FIG. 2  is a flowchart of a process procedure for the biologically-active-substance candidate structure generation method according to the embodiment. A three-dimensional structure of the protein is determined first (at a step S 201 ), and the target active site  102  of the protein is determined (at a step S 202 ).  
      A fragment set of the compound fragments to be packed (input) are selected from the fragment library  101  (at a step S 203 ). The selected fragment set is input into the active site  102  (at a step S 204 ), and an MD calculation is performed so as to stably locate the input fragment set in the active site  102 . In order to stably locate the input fragment set, it is necessary to set “positions” and “orientations” of the fragments relative to the active site.  
      Thereafter, while the fragments are stably located as obtained, pseudo monoatoms are packed (input) into the active site, and their respective binding probabilities are evaluated (at a step S 206 ). A molecular scaffold by binding is constructed (at a step S 207 ), heteroatom substituent candidates are selected (at a step S 208 ), and the pseudo monoatoms are substituted with the selected heteroatoms (at a step S 209 ). At this time, energy calculation is performed while the pseudo monoatoms are substituted with the selected heteroatoms (at a step S 210 ), and it is confirmed that the pseudo monoatoms are substituted with the selected heteroatoms (at a step S 211 ). Finally, a final candidate structure is confirmed (at a step S 212 ), and a series of processings are finished.  
       FIG. 3  is a schematic for illustrating an example of a hardware configuration of a biologically-active-substance candidate structure generating apparatus according to the embodiment.  
      A biologically-active-substance candidate structure generating apparatus includes a central processing unit (CPU)  301 , a read only memory (ROM)  302 , a random access memory (RAM)  303 , a hard disk drive (HDD)  304 , a hard disk (HD)  305 , a flexible disk drive (FDD)  306 , a flexible disk (FD)  307  that is one example of a detachable recording medium, a display  308 , an interface (I/F)  309 , a keyboard  311 , a mouse  312 , a scanner  313 , and a printer  314 . The respective constituent elements of the apparatus are connected to one another by a bus  300 .  
      The CPU  301  controls entirety of the biologically-active-substance candidate structure generating apparatus. The ROM  302  stores programs such as a boot program. The RAM  303  is used as a work area for the CPU  301 . The HDD  304  controls read and write of data from and to the HDD  305  under control of the CPU  301 . The HD  305  stores the written data under control of the HDD  304 .  
      The FDD  306  controls read and write of data from and to the FD  307  under control of the CPU  301 . The FD  307  stores the written data under control of the FDD  306 , and reads the data recorded in the FD  307  to an information processing apparatus. As the detachable recording medium, a CD-ROM (CD-R or CD-RW), a magneto-optical (MO) disk, a digital versatile disk (DVD), a memory card, or the like may be employed instead of the FD  307 . The display  308  displays data such as a document, an image, and functional information as well as cursors, icons, or tool boxes. The display  308  is, for example, a cathode ray tube (CRT), a thin film transistor (TFT) liquid crystal display (LCD), or a plasma display panel (PDP).  
      The I/F  309  is connected to a network  310  such as a local area network (LAN) or the Internet through a communication line, and connected to the other server or the information processing apparatus including a database and the like through the network  310 . The I/F  309  interfaces the network  310  with the constituent elements of the biologically-active-substance candidate structure generating apparatus, and controls input and output of data from and to the other server or an information terminal apparatus. The I/F  309  is, for example, a modem or a LAN adapter.  
      The keyboard  311  includes keys used to input characters, numbers, various instructions, and the like, and inputs data. The keyboard  311  may be replaced by a touch-panel input pad or a numeric keypad. The mouse  312  performs a cursor movement, a range selection, a window movement, a size change, and the like. The mouse  312  may be replaced by a trackball, a joystick, or the like as long as it functions equally to the mouse  312  as a pointing device.  
      The scanner  313  optically reads an image such as a driver image and fetches image data into the information processing apparatus. The scanner  313  also has an optical character recognition (OCR) function, and can read printed information and convert the read information into data by the OCR function. The printer  314  prints image data and document data. The printer  314  is, for example, a laser printer or an inkjet printer.  
       FIG. 4  is a schematic for illustrating a functional configuration of the biologically-active-substance candidate structure generating apparatus according to the embodiment.  
      The biologically-active-substance candidate structure generating apparatus includes a fragment selecting unit  401 , an MD calculating unit  402 , a monoatom inputting and binding probability evaluating unit  403 , a molecular scaffold constructing unit  404 , and a heteroatom substituting unit  405 .  
      The fragment selecting unit  401  selects arbitrary compound fragments from the fragment library  101 . At this moment, the fragment selecting unit  401  selects so-called large fragments each having a predetermined number of atoms or more and a predetermined volume or more, and then selects so-called small fragments each having the number of atoms less than the predetermined number of atoms and a volume less than the predetermined volume.  
      The MD calculating unit  402  conducts a location search using the molecular dynamics calculation (e.g., MD calculation) based on protein three-dimensional information  410  and active site information  420  so as to stably locate the fragments selected by the fragment selecting unit  401  in the active site of the protein. As a result, stable locations of the fragments can be obtained.  
      The monoatom inputting and binding probability evaluating unit  403  inputs pseudo monoatoms into the active site in which the arbitrary fragments are stably located, and evaluates (determines) binding probabilities of bonding between the fragments, bonding between the fragment and the monoatom, and bonding between the monoatoms. Specifically, the monoatom inputting and binding probability evaluating unit  403  determines the binding probabilities based on whether at least, for example, atomic distances and bond angles are within their allowable ranges.  
      The molecular scaffold constructing unit  404  constructs a molecular scaffold by bonding the fragments together, bonding the fragment and the monoatom, and bonding the monoatoms together based on an evaluation result of the monoatom inputting and binding probability evaluating unit  403 .  
      The heteroatom substituting unit  405  substitutes the pseudo atoms, for which the molecular scaffold is constructed by the molecular scaffold constructing unit  404 , with heteroatoms. Specifically, based on, for example, a fluctuation in energy of an electrostatic interaction, the heteroatom substituting unit  405  determines whether substitution with the heteroatoms is effective, and substitutes the pseudo atoms with the heteroatoms based on the determination result.  
      The functions of the fragment selecting unit  401 , the MD calculating unit  402 , the monoatom inputting and binding probability evaluating unit  403 , the molecular scaffold constructing unit  404 , and the heteroatom substituting unit  405  are realized specifically when, for example, the CPU  301  executes the program recorded in the ROM  302 , the RAM  303 , the HD  305  or FD  307  shown in  FIG. 3 .  
      The fragment library  101  is composed by, for example, a first library for real atoms (carbon atoms and heteroatoms) and a second library for pseudo monoatoms obtained by converting all the real atoms.  
      The first library for the real atoms (carbon atoms and heteroatoms) is a database which stores partial structures that appear in biologically-active-substances such as existing medical, agricultural, and pharmaceutical products with high frequency in the form of molecular structural formulas (three-dimensional coordinates). Further, since amino acids are often applied as constituent elements of medical and pharmaceutical products, side chains of  20  types of amino acids may be stored in the first library. A minimum unit is a C of an alanine side chain (one carbon atom).  
      In addition, the second library for the pseudo monoatoms converted from all the real atoms of the first library stores, for example, only patterns such as three-membered, four-membered, five-membered, six-membered, and seven-membered rings, condensed rings, linear scaffolds, and monoatoms. Specifically, the function of the fragment library  101  is realized by, for example, the HD  305  and the FD  307  shown in  FIG. 3 . Further, the fragment library  101  may be included in, for example, the other information processing apparatus connected to the biologically-active-substance candidate structure generating apparatus through the I/F  309  by the network  310  shown in  FIG. 3 .  
       FIG. 5  is a flowchart of a process procedure for a fragment selecting processing according to the embodiment. It is assumed that a rectangular parallelepiped which accommodates the active site  102  of a target protein is present, and the number of atoms accommodated in the rectangular parallelepiped is calculated (at a step S 501 ).  
      Several large-sized fragments (large fragments), specifically, fragments each having a predetermined number of atoms or more or a predetermined volume or more are randomly selected (at a step S 502 ). The large fragments are normally cyclic compounds or the like. It is determined whether a total number of atoms account for an accommodation capacity of, for example, about 30% of the number of atoms accommodated in the rectangular parallelepiped (at a step S 503 ). The selection is continued until the accommodation capacity reaches about 30%. If the accommodation capacity reaches about 30% (“Yes” at the step S 503 ), the small fragments are randomly selected (at a step S 504 ) and the small fragments are added until the accommodation capacity reaches about 50%.  
      If the accommodation capacity reaches about 50% (“Yes” at the step S 505 ), the result is stored (at a step S 506 ). It is then determined whether a preset predetermined number of fragment sets are selected (at a step S 507 ). If the predetermined number of fragment sets are not selected yet (“No” at the step S 507 ), the processing returns to the step S 502 . Thereafter, the steps S 502  to S 507  are repeatedly executed. If the predetermined number of fragment sets are selected (“Yes” at the step S 507 ), a series of processings are finished.  
      It is noted that 30% and 50% explained above are examples, and that optimum values may be selected according to a state of the active site and the type of fragments to be input.  
      An initial packing quantity is set at, for example, 180 fragments/nm 3  when the rectangular parallelepiped is most closely packed in the form of diamond (at a density of 3.51 g/cm 3 ). However, the most closely packed rectangular parallelepiped is too dense, so that the initial packing quantity can be set in a range of 30 fragments/nm 3  to 90 fragments/nm 3 . In addition, if the protein is an HIV protease inhibitor (PDB: 1D4H), an active site space has a volume of about 0.8 nm 3  and the inhibitor has 44 atoms (except for hydrogen atoms). Therefore, the initial packing quantity is 55 fragments/nm 3 . For most of drugs (finally packed state), the initial packing quantity is set at about 55 fragments/nm 3 . In this embodiment, the initial packing quantity is far smaller than 55 fragments/nm 3 , i.e., about 20 fragments/nm 3  to 40 fragments/nm 3 . In this state, monoatoms are packed into the rectangular parallelepiped.  
       FIG. 6  is a flowchart of a process procedure for an MD calculation processing according to the embodiment. One fragment set is randomly extracted from the selected predetermined number of fragment sets (at a step S 601 ). The fragments are appropriately located in the active site (at a step S 602 ).  
      An MD calculation based on an interaction between the protein and the compound and an interaction between the fragments is executed (at a step S 603 ). Only the interaction between the protein and the fragment is evaluated and it is determined whether the interaction is higher than a predetermined index (at a step S 604 ). If the interaction is higher than the predetermined index (“Yes” at the step S 604 ), the result is stored (at a step S 605 ). If the interaction is lower than the predetermined index (“No” at the step S 604 ), no processing is performed.  
      As a result, the fragments which are located in an area relatively close to a lining wall of the protein remain. If a calculation time is short, then all fragments cannot be searched and the result may possibly depend on the initial location of the fragments (a relative position and a direction of each fragment) in the protein active site. The MD calculation may be performed for the fragments having different initial location patterns.  
      It is determined whether all the predetermined number of fragments is completed with the processing (at a step S 606 ). If all the predetermined number of fragments are not completed with the processing (“No” at the step S 606 ), the processing returns to the step S 601 . Thereafter, the steps S 601  to S 606  are repeatedly executed. At the step S 606 , if all the predetermined number of fragments is completed with the processing (“Yes” at the step S 606 ), a series of processings are finished.  
      In the present embodiment, after the predetermined number of fragment sets are selected, the MD calculation processing is performed. Alternatively, the MD calculation processing may be performed whenever fragments are selected.  
       FIG. 7  is a flowchart of a process procedure for monoatoms locating, binding probability estimation, and molecular scaffold construction processing according to the embodiment. Two fragments for which the atomic distance and the bond angle are within stereochemically allowable ranges, respectively are searched (at a step S 701 ).  
      If the atomic distance and the bond angle of the fragments are within their respective stereochemically allowable ranges (“Yes” at the step S 701 ), the fragments are bonded together (at a step S 702 ). If the atomic distance and the bond angle thereof are not within stereochemically allowable ranges (“No” at the step S 701 ) and the fragments are too close (“Yes” at a step S 703 ), the fragments are excluded from candidates and the processing is finished. If the atomic distance and the bond angle thereof are not within stereochemically allowable ranges (“No” at the step S 701 ) and the fragments are away from each other (“No” at a step S 703 ), no processing is performed. It is determined whether all fragments have been bonded together (at a step S 704 ). If all fragments have not been bonded yet (“No” at the step S 704 ), the processing returns to the step S 701 .  
      If all fragments have been bonded together (“Yes” at the step S 704 ), many gaps are present everywhere only with the fragments located in the active site. Therefore, to fill the gaps, monoatoms are input (at a step S 705 ) and a location at which the binding probability can be expected is searched. Specifically, one atom is input at an arbitrary location, and it is determined whether a new bonding distance and a new bond angle formed between the input atom and a certain atom of the fragment already located or a monoatom input after the one atom are within appropriate ranges (at a step S 706 ).  
      Whether the new bonding distance and the new bond angle are within their respective appropriate ranges is determined based on, for example, conditions for determining whether a pseudo atom can be located as shown in  FIG. 8 . Specifically, while the bonding distance is set at, for example, 0.12 nm to 0.16 nm and the bond angle is set at, for example, 100 degrees to 130 degrees, all atoms which can be bonded with the one atom are searched. For the bond angle, it is determined whether a bond angle formed between a newly formed bond and an originally present bond ahead of the new bond is within the allowable range.  FIG. 9  is a schematic for illustrating a content of the condition ( 5 ) in the table shown in  FIG. 8 . The condition ( 5 ) in the table indicates that if a tried location position is a, then Rab and Rae are within the allowable range, and θbae, θabc, θabd, and θaef are within the allowable range, and that Daj, Dak, and the like are equal to or larger than a limited distance (within the allowable range). Symbols Rab, Rae, Daj, and Dak denote distances between a and b, a and e, a and j, and a and k, respectively, and symbols θbae, θabc, θabd, and θaef denote angles formed between ba and ea, ab and cb, ab and db, and ae and fe, respectively.  
      If the bond angles and the bonding distances are within their respective appropriate ranges (“Yes” at the step S 706 ), the one atom is coupled with all the other atoms (at a step S 707 ). If they are not within the respective appropriate ranges (“No” at the step S 706 ), the processing is finished. Further, a monoatom which may possibly be bonded is bonded with a certain atom of a fragment or another monoatom. If a plurality of candidate atoms bonded with the monoatom for which the bonding distances and the bond angles are within the allowable ranges are present, all of the candidate atoms are bonded with the one monoatom. For the one atom, bonding distances and bond angles are similarly calculated and binding probabilities are calculated for an atom (a part of the fragment or another monoatom) ahead of the one atom. If it is determined that candidates can be bonded with the atom, they are bonded together.  
      If the processings are repeatedly executed (“Yes” at a step S 708 ), gaps are smaller and smaller. At the same time, fragments and monoatoms are gradually bonded, so that the structure is larger. If no new bond is generated anywhere after repeating the processings at the steps S 705  to S 707  (“No” at the step S 708 ), a series of processings are finished.  
       FIG. 10  is a flowchart of a process procedure for the heteroatom substituent candidate selection, hetero atom substitution estimation, and determination processing according to the embodiment.  
      A correlation between an atom and an amino acid of the protein is observed and the atom is substituted with a heteroatom suitable for an interaction with the amino acid (at a step S 1001 ). A negatively charged atom is located for a positively charged atom or vice versa, or an atom which serves as a hydrogen-bond acceptor is located for an atom which serves as a hydrogen-bond donor or vice versa. If N, O, S, P, F, Cl, Br, or the like is a substituent candidate (“Yes” at a step S 1002 ), the atom is substituted with the substituent candidate (at a step S 1003 ). Otherwise (“No” at the step S 1002 ), the atom is substituted with a carbon atom (at a step S 1004 ).  
      For heteroatom substitution, it is normally considered that many candidates are present. Attention is paid to one of the candidates, and energy of an electrostatic interaction is calculated so as to determine whether substitution of the atom with a certain heteroatom is effective (at a step S 1005 ). The effectiveness is evaluated based on a fluctuation in the calculated energy. If the substitution is effective, that is, the energy is reduced (“Yes” at the step S 1006 ), the substitution is adopted and it is confirmed that the atom is substituted wit the heteroatom (at a step S 1007 ). If it is not effective (“No” at the step S 1006 ), the substitution is not adopted and the processing moves to a step S 1008 . Thereafter, similar operation is continued for the other location (“No” at a step S 1008 ). If all the candidates are completed with the processing (“Yes” at the step S 1008 ), a series of processings are finished.  
      Since a dihedral angle is not considered so far, the candidates which have abnormal dihedral angles are excluded. In addition, in order to evaluate overall docking with the protein, free bonding energies are calculated and checked. Further, by making final confirmation based on an index of Drug-likeness such as Lipinsk rule, atoms which cannot be expected to serve as candidates are excluded. As a result, the final candidate structure can be confirmed.  
      As explained so far, with the method and the apparatus for generating biologically-active-substance candidate structure and the computer product according to the embodiment, fragments of an arbitrary compound are selected, the selected fragments are stably located in the active site of the protein, pseudo monoatoms are input into the active site in which the arbitrary fragments are stably located, the molecular scaffold based on bonding between the fragments, bonding between the fragment and the monoatom, and bonding between the monoatoms is constructed, and the pseudo monoatoms, for which the molecular scaffold is constructed, are substituted with heteroatoms. Therefore, a candidate ligand compound (e.g., an inhibitor) to be bonded with a protein (e.g., enzyme) having a known three-dimensional structure can be designed de novo. Further, according to the embodiment, in a process of searching candidate compounds which control (inhibit or promote) functions of the known protein, a hit ratio can be improved, a search time can be shortened, and a cost reduction can be realized.  
      The biologically-active-substance candidate structure generation method explained in the embodiment can be realized by allowing a computer such as a personal computer or a workstation to execute a program prepared in advance. The program is recorded in a computer readable recording medium such as a hard disk, a flexible disk, a CD-ROM, an MO disk, or a DVD, and executed by reading the program. Alternatively, this program may be a transmission medium which can be distributed through a network such as the Internet.  
      An example of the embodiment is as follows. 
      1. Materials    

      Protein: HIV protease (PDB number: 1D4H)  
      Drug: Inhibitor (Bea435, C36H38N2O7)  
      A ligand in an X-ray co-crystal structure is divided into fragments and it is examined whether a similar location of the fragments can be reproduced by the method according to the embodiment.  
     
         
          2. Set potential  
       
    
      Fragments: Partial structure of a rigid body (zero internal flexibility)  
      Atomic species: Pseudo atoms (mass of 20.179)  
      Potential: A potential with which only van der Waals force acts between the lining wall of the protein and the fragment and between the fragments is set (the following Leonard-Jones potential is used).  
      Leonard-Jones Potential 
 
 E   VDW =ε ij [(σ ij   /r ) 12 −2(σ ij   /r ) 6 ]   (1) 
 
 where E VDW : van der Waals energy 
          r: Atomic distance     εvv: Pseudo atom, parameter between pseudo atoms     σvv: Pseudo atom, parameter between pseudo atoms     ε VP : Pseudo atom, parameter between protein atoms     σ VP : Pseudo atom, parameter between protein atoms         3. Molecular dynamics method    

      Software: TINKER  
      Calculation TimeStep: 1 fs  
      Calculation time: 20 ps  
      Temperature: 298K  
      Initial location: four cyclic structures of the 1D4H inhibitor are selected with positions and orientation set randomly.  
      Other conditions:  
      Step1: MM under the following conditions. 
 
ε VV =0.755, σ VV =0.01, ε VP =3.45, and σ VP =0.02 
 
      Step2: MD for 20 ps under the following conditions. 
 
ε VV =0.755, σ VV =0.01, ε VP =3.45, σ VP =2.0, and temperature of 298° K 
 
      Step3: MD for 20 ps under the following conditions. 
 
ε VV =0.755, σ VV =0.01, ε VP =3.45, σ VP =2.06, and temperature of 298° K 
      4. Result and evaluation    

      The following result is obtained when the initial location is changed and the processing is performed.  FIG. 11A  is a schematic for illustrating a state of a measured location on x-y plane; and  FIG. 11B  is a schematic for illustrating a state of a measured location on x-z plane.  FIG. 12A  is a schematic for illustrating a state of a packing result on x-y plane; and  FIG. 12B  is a schematic for illustrating a state of a packing result on x-z plane.  
       FIG. 13  is a schematic for explaining an example of a known inhibitor structure.  FIG. 14  is a schematic for explaining first example of a candidate ligand structure.  FIG. 15  is a schematic for explaining second example of the candidate ligand structure.  FIG. 16  is a schematic for explaining third example of the candidate ligand structure.  FIG. 17  is a schematic of a three-dimensional structure of the known inhibitor shown in  FIG. 13 .  FIG. 18  is a schematic of a three-dimensional structure of the candidate ligand shown in  FIG. 14 . According to the embodiment, the location quite similar to the measured location of the cyclic structure can be obtained.  
      The present invention exhibits effects of obtaining a biologically-active-substance candidate structure generation program, a biologically-active-substance candidate structure generation method, and a biologically-active-substance candidate structure generating apparatus capable of efficiently generating an appropriate biologically-active-substance candidate structure.  
      Although the invention has been described with respect to a specific embodiment for a complete and clear disclosure, the appended claims are not to be thus limited but are to be construed as embodying all modifications and alternative constructions that may occur to one skilled in the art which fairly fall within the basic teaching herein set forth.