CN107301327A - A kind of method that use computer simulation metal complex interacts with DNA - Google Patents
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Abstract
The invention discloses a kind of method that use computer simulation metal complex and DNA interact.Interaction of this method using Gaussian softwares and Autodock docking softwares on a common computer to metal complex and DNA is simulated.Structure first to metal complex in Gaussian softwares is optimized, and is used as ligand molecular；Then metal complex and DNA molecular docking are carried out in AutoDock softwares, finally docking result is analyzed.The inventive method need not be by means of huge computer servers, it can run on a common computer, equipment cost is very low, CPU core number required in calculating process is low, committed memory is small, time used in the process entirely calculated is very short and analog result is reliable, contributes to the extensive use in fields such as biochemistry, Coordinative Chemistry, biological medicines.
Description
Technical field
The present invention relates to computer simulation biochemical reaction process technical field, and in particular to one kind uses computer simulation gold
The method that metal complex interacts with DNA.
Background technology
Many cancer therapy drugs generally using DNA as important targeting target, by being interacted with DNA so as to influenceing cancer thin
A series of physiological activities of born of the same parents, such as the transcription of DNA replicates synthesis with protein etc..Cancer therapy drug still lacks to targeting DNA
Weary high efficiency and specificity, the interaction for probing into cancer therapy drug and DNA is extremely important.It is experimentally ultraviolet by UV-vis
The methods such as visible spectrum, circular dichroism, fusing point test, viscosity measurement and colloidal sol electrophoresis can study metal complex with
DNA interaction, but specific combination conformation can not be drawn and the mechanism of action is explained.Because experimental study has necessarily
Limitation, therefore simulated by molecular docking metal complex and DNA interaction is studied, will be in area of computer aided
Played a great role in terms of drug design.
Molecular docking simulation is exactly the position of ligand molecular identification receptor molecular activity combination, according to energy complement, several
What complementary and chemical environment complementarity principle assesses the repercussion effect of ligand molecular and acceptor molecule, and searches for and match somebody with somebody
Best incorporated conformation between body molecule and acceptor molecule.Many molecular docking softwares are required in mainframe computer service at present
Run on device, and the molecular structure of part is not readily available.Therefore based on case above, using combine Gaussian softwares and
Interaction of the Autodock docking software on a common computer to metal complex and DNA carries out simulation calculating.It is right first
Metal complex carries out structure optimization in Gaussian softwares, the accurate structural of part can be obtained, then in AutoDock
Using more excellent Lamarckian genetic algorithm to metal in software (including AutoDock subprograms and AutoGrid subprograms)
Complex carries out molecular simulation with DNA and docked, and can improve the degree of accuracy, and docking result finally is carried out into arrangement analysis.
The content of the invention
In view of the deficiencies of the prior art, the present invention provides a kind of use computer simulation metal complex and DNA are mutual
The method of effect.This invention address that carrying out gold on a common computer using Gaussian softwares and Autodock docking softwares
The simulation that metal complex interacts with DNA.Structure optimization is carried out in Gaussian softwares to metal complex first, as
Ligand molecular；Then metal complex and DNA molecular docking are carried out in AutoDock softwares.
The present invention is achieved through the following technical solutions.
A kind of method that use computer simulation metal complex interacts with DNA, comprises the following steps：
(1) structure optimization of metal complex：In Gaussian softwares, using DFT method B3LYP functionals and use
Mixed base group, the metal complex structure to drafting carries out geometric hash, obtains the accurate structural of metal complex；
DFT method can obtain preferable result to the Geometrical optimization of metal complex, and wherein B3LYP functionals optimize
Geometry is more reasonable；
(2) structure of the region of search of ligand conformational：In AutoDock softwares, using DNA as acceptor molecule, to surround
The active binding site of acceptor constitutes lattice point box as the region of search of ligand conformational, and is probe with different types of atom
Lattice point energy is scanned and calculates to calculate the interaction energy between probe atom and acceptor；
(3) molecular docking：Metal complex after structure optimization is as ligand molecular, with AutoDock softwares
AutoGrid subprograms be lattice point formula searching method, ligand conformational region of search search active binding site, make acceptor with
The molecular docking of part；Finally metal complex in AutoDock subprograms repeatedly dock with DNA and calculate and search
Rope best combination position, the docking result finally given is analyzed.
Further, in step (1), metal complex is most stable under ground state, carries out the metal complex of structure optimization
For the metal complex in ground state.
Further, in step (1), in the mixed base group, the light atom including hydrogen, carbon, nitrogen and oxygen is used
6-31G** base groups, heavy metal atom uses LanL2DZ base groups.
Further, in step (1), the metal complex after structure optimization saves as PDB formatted files.
Further, in step (2), the crystal structure of the DNA is derived from Protein Data Bank, and simulation process
DNA structure deletes the crystallization water and ion, and the DNA crystal structures of acquisition do not include the coordinate data of hydrogen atom, add all
Hydrogen atom.
Further, in step (2), the region of search of the ligand conformational includes whole DNA molecular structure, it is ensured that metal
Complex can be combined with each other with DNA any part.
Further, in step (2), in the region of search of the ligand conformational, lattice point at intervals of default value
0.0375nm。
Further, in step (2), the different types of atom includes tri- kinds of atoms of C, H and O
Further, in step (2), the calculating lattice point energy, mainly by the AutoGrid in AutoDock softwares
Subprogram is calculated.
Further, in step (3), the computational methods of the docking are the Lamarch heredity calculation in AutoDock softwares
Method.
Further, in step (3), the docking operation is carried out under default temperature 298.15K.
Compared with prior art, the present invention has advantages below and beneficial effect：
(1) present invention carries out Geometrical optimization by using Gaussian softwares to metal complex, and can paint
Specific ligand structure is made, the geometric configuration after optimization is more accurate reasonable；
(2) Autodock of the invention docking software uses Lamarckian genetic algorithm, and the algorithm compares simulated annealing
It is as a result also relatively reliable and other traditional algorithms have higher efficiency；
(3) Autodock of the invention docking software can be run on a common computer, in Windows systems and
It can be installed in linux system, equipment cost is very low, and occupancy CPU core number and internal memory are small, operating efficiency is high；
(4) operational efficiency of the invention is very high, even the calculating of 200 conformations of operation also can be complete within a short period of time
Into, and analog result is reliable, contributes to the extensive use in fields such as biochemistry, Coordinative Chemistry, biological medicines；
(5) present invention especially Van der Waals force, hydrogen bond and removes solvent primarily directed to the calculating of intermolecular interaction
The calculating precision of change effect is high, and metal complex can mostly come from the contribution of these effects with DNA interactions；
(6) docking information that result of calculation of the invention is shown is very abundant, can directly observe metal complex and DNA
With reference to conformation, Conjugated free energy, intermolecular interaction energy, van der Waals energy, hydrogen bond energy included in docking result, solvent is removed
Change a series of energy such as energy, electrostatic energy, distortional energy, final total interior energy and nonbonding system energy to be clearly shown out.
Brief description of the drawings
Fig. 1 is that metal complex and DNA dock illustraton of model.
Embodiment
With reference to embodiment and accompanying drawing, the present invention is further illustrated, but protection scope of the present invention is not limited to
This.
The region of search of ligand conformational is X × Y × Z cuboid box in the specific embodiment of the invention, and maximum
It may be configured as 126 × 126 × 126.
The search parameter of the genetic algorithm set in the specific embodiment of the invention is as shown in table 1.
The major parameter of the genetic algorithm of table 1 is set
Embodiment 1
Complex and DNA interaction are coughed up using computer simulation manganese metal click, is run in Windows systems, tool
Body step is as follows：
(1) the manganese metal click of selection ground state coughs up complex (four pyrroles by the big ring of three methylene-bridgeds, matches somebody with somebody by center
Position metal manganese atom) as ligand molecular, draw after manganese metal click coughs up the molecular structure of complex to enter in Gaussian softwares
Row geometric hash；Complex progress is coughed up to manganese metal click using the B3LYP functionals and mixed base group in DFT method excellent
Change, at this series of light atoms such as hydrogen, carbon, nitrogen are used with 6-31G** base groups, metal manganese atom uses LanL2DZ base groups；In base
Complex is coughed up under state to manganese metal click and carries out Geometrical optimization, the file of Mncor.pdb titles is then saved as, as next
Walk the ligand molecular of molecular docking；
(2) acceptor molecule is pre-processed：Acceptor molecule is from Protein Data Bank (such as http://
Www.rcsb.org/pdb/home/home.do downloaded on), PDB files are 3U2N.pdb；Open AutoDock Tools couple
Connect software, the working directory of All Files is set, then by Autogrid subprograms and Autodock subprograms and the PDB of download
File is copied in the working directory；Acceptor molecule is imported, then removes the crystallization water and ion on DNA, and add all
Hydrogen atom (the DNA crystal structures that X-ray diffraction is obtained do not include the coordinate data of hydrogen atom), finally preserves the acceptor changed
Molecule；
(3) ligand molecular is pre-processed：The ligand molecular of PDB forms is imported at menu, the molecule is carried out just
Beginningization, takes default value, is saved as containing atomic coordinates, AutoDock atomic types, electric charge and can reverse the letter such as key
The file of the Mncor.pdbqt titles of breath；
(4) Autogrid subprograms are run：Ready acceptor molecule and ligand molecular text before selecting in a menu
Part, opens lattice point options dialog box and sets lattice point box, grid is dimensioned into 60 × 60 × 100, lattice point is at intervals of silent
Recognize value, grid center is set to DNA, the lattice point parameter set is saved as into GPF files；Change host name, journey
Sequence path and title, autogrid subprograms, Parameter File and log file, operation program are calculated；
(5) Autodock subprograms are run：Acceptor molecule 3U2N.pdbqt and ligand molecular in selection docking are
Mncor.pdbqt, sets the search parameter (being shown in Table 1) of genetic algorithm, carries out 200 stable conformations；Set using system default value
Put docking operational factor, output Lamarckian genetic algorithm docking Parameter File dock.dpf；Start AutoDock graphical interfaces, repair
Change autodock subprograms, Parameter File and log file, carry out docking calculating and search for best combination position, will be final
Obtained docking result is saved in log file dock.dlg；
(6) interpretation of result is docked, docking log file dock.dlg is opened, shown in this journal file comprising docking result
Molecular conformation and data：DNA molecular is loaded into graphical interfaces, display manganese metal click coughs up docking for complex and DNA
Conformation and Conjugated free energy；
The illustraton of model of docking is as shown in figure 1, Fig. 1 shows that manganese metal click coughs up complex with DNA mainly in combination with ditch position.
The Conjugated free energy analysis result for docking 5 conformations of result formation is as shown in table 2.
(unit is kcalmol to the analysis of the Conjugated free energy of table 2-1)
Table 2 show manganese metal click cough up the interaction between complex and DNA mostly come from Van der Waals force, hydrogen bond and
Desolvation interacts, and the contribution of electrostatic interaction is seldom.
The molecular conformation for docking result is clustered, to be analyzed result and be compared, the result such as institute of table 3 of cluster
Show.
(unit is kcalmol to the cluster result of table 3-1)
Table 3 shows that Conjugated free energy is -8.18kcalmol-1Conformation 2 have most molecular conformation quantity, explanation
It is most stable under the state of conformation 2 that manganese metal click coughs up complex.
Embodiment 2
Complex and DNA interaction are coughed up using computer simulation gallium click, is run in Windows systems, tool
Body step is as follows：
(1) the gallium click of selection ground state coughs up complex (four pyrroles by the big ring of three methylene-bridgeds, matches somebody with somebody by center
Position gallium atom) as ligand molecular, draw after gallium click coughs up the molecular structure of complex to enter in Gaussian softwares
Row geometric hash；Complex progress is coughed up to gallium click using the B3LYP functionals and mixed base group in DFT method excellent
Change, at this series of light atoms such as hydrogen, carbon, nitrogen are used with 6-31G** base groups, gallium atom uses LanL2DZ base groups；In base
Complex is coughed up under state to gallium click and carries out Geometrical optimization, the file of Gacor.pdb titles is then saved as, as next
Walk the ligand molecular of molecular docking；
(2) acceptor molecule is pre-processed：Acceptor molecule is from Protein Data Bank (such as http://
Www.rcsb.org/pdb/home/home.do downloaded on), PDB files are 2GVR.pdb；Open AutoDock Tools couple
Connect software, the working directory of All Files is set, then by Autogrid subprograms and Autodock subprograms and the PDB of download
File is copied in the working directory；Acceptor molecule is imported, then removes part, the crystallization water and the ion on DNA, and add institute
Some hydrogen atoms (the DNA crystal structures that X-ray diffraction is obtained do not include the coordinate data of hydrogen atom), finally preserve what is changed
Acceptor molecule；
(3) ligand molecular is pre-processed：The ligand molecular of PDB forms is imported at menu, the molecule is carried out just
Beginningization, takes default value, is saved as containing atomic coordinates, AutoDock atomic types, electric charge and can reverse the letter such as key
The file of the Gacor.pdbqt titles of breath；
(4) Autogrid subprograms are run：Ready acceptor molecule and ligand molecular text before selecting in a menu
Part, opens lattice point options dialog box and sets lattice point box, grid is dimensioned into 60 × 60 × 120, lattice point is at intervals of silent
Recognize valueGrid center is set to DNA, the lattice point parameter set is saved as into GPF files；Change host name, program
Path and title, autogrid subprograms, Parameter File and log file, operation program are calculated；
(5) Autodock subprograms are run：Acceptor molecule 2GVR.pdbqt and ligand molecular in selection docking are
Gacor.pdbqt, sets the search parameter (being shown in Table 1) of genetic algorithm, carries out 200 stable conformations；Set using system default value
Put docking operational factor, output Lamarckian genetic algorithm docking Parameter File dock.dpf；Start AutoDock graphical interfaces, repair
Change autodock subprograms, Parameter File and log file, carry out docking calculating and search for best combination position, will be final
Obtained docking result is saved in log file dock.dlg；
(6) interpretation of result is docked, docking log file dock.dlg is opened, shown in this journal file comprising docking result
Molecular conformation and data：DNA molecular is loaded into graphical interfaces, display gallium click coughs up docking for complex and DNA
Conformation and Conjugated free energy；
The illustraton of model of docking coughs up complex with DNA mainly in combination with ditch position referring to Fig. 1, display gallium click.
The Conjugated free energy analysis result for docking 5 conformations of result formation is as shown in table 4.
(unit is kcalmol to the analysis of the Conjugated free energy of table 4-1)
Table 4 shows that gallium click coughs up complex and DNA interaction mostlys come from Van der Waals force, hydrogen bond and gone molten
Agentization interacts, and the contribution of electrostatic interaction is seldom.
The molecular conformation for docking result is clustered, to be analyzed result and be compared, the cluster result such as institute of table 5
Show.
(unit is kcalmol to the cluster result of table 5-1)
Table 5 shows that Conjugated free energy is -8.06kcalmol-1Conformation 2 have most molecular conformation quantity, explanation
It is most stable under the state of conformation 2 that gallium click coughs up complex.
Embodiment 3
Using computer simulation manganese metal metalloporphyrin complex and DNA interaction, run in Windows systems, tool
Body step is as follows：
(1) the manganese metal metalloporphyrin complex of selection ground state (by the big ring of four methylene-bridgeds, match somebody with somebody four pyrroles by center
Position metal manganese atom) as ligand molecular, enter after the molecular structure for drawing manganese metal metalloporphyrin complex in Gaussian softwares
Row geometric hash；Complex progress is coughed up to manganese metal click using the B3LYP functionals and mixed base group in DFT method excellent
Change, at this series of light atoms such as hydrogen, carbon, nitrogen are used with 6-31G** base groups, metal manganese atom uses LanL2DZ base groups；In base
Geometrical optimization is carried out to manganese metal metalloporphyrin complex under state, the file of Mnpor.pdb titles is then saved as, as next
Walk the ligand molecular of molecular docking；
(2) acceptor molecule is pre-processed：Acceptor molecule is from Protein Data Bank (http://www.rcsb.org/
Pdb/home/home.do downloaded on), PDB files are 3U05.pdb；AutoDock Tools docking softwares are opened, institute is set
Documentary working directory, then the PDB files of Autogrid subprograms and Autodock subprograms and download are copied to this
In working directory；Acceptor molecule is imported, then removes the crystallization water and ion on DNA, and add all hydrogen atom (X-rays
The DNA crystal structures that diffraction is obtained do not include the coordinate data of hydrogen atom), finally preserve the acceptor molecule changed；
(3) ligand molecular is pre-processed：The ligand molecular of PDB forms is imported at menu, the molecule is carried out just
Beginningization, takes default value, is saved as containing atomic coordinates, AutoDock atomic types, electric charge and can reverse the letter such as key
The file of the Mnpor.pdbqt titles of breath；
(4) Autogrid subprograms are run：Ready acceptor molecule and ligand molecular text before selecting in a menu
Part, opens lattice point options dialog box and sets lattice point box, grid is dimensioned into 60 × 60 × 100, lattice point is at intervals of silent
Recognize value, grid center is set to DNA, the lattice point parameter set is saved as into GPF files；Change host name, journey
Sequence path and title, autogrid subprograms, Parameter File and log file, operation program are calculated；
(5) Autodock subprograms are run：Acceptor molecule 3U05.pdbqt and ligand molecular in selection docking are
Mnpor.pdbqt, sets the search parameter (being shown in Table 1) of genetic algorithm, carries out 200 stable conformations；Set using system default value
Put docking operational factor, output Lamarckian genetic algorithm docking Parameter File dock.dpf；Start AutoDock graphical interfaces, repair
Change autodock subprograms, Parameter File and log file, carry out docking calculating and search for best combination position, will be final
Obtained docking result is saved in log file dock.dlg；
(6) interpretation of result is docked, docking log file dock.dlg is opened, shown in this journal file comprising docking result
Molecular conformation and data：DNA molecular is loaded into graphical interfaces, display manganese metal metalloporphyrin complex is docked with DNA's
Conformation and Conjugated free energy；
The illustraton of model of docking is referring to Fig. 1, and display manganese metal metalloporphyrin complex is with DNA mainly in combination with ditch position.
The Conjugated free energy analysis result for docking 5 conformations of result formation is as shown in table 6.
(unit is kcalmol to the analysis of the Conjugated free energy of table 6-1)
Table 6 shows that manganese metal metalloporphyrin complex and DNA interaction mostly come from Van der Waals force, hydrogen bond and gone molten
Agentization interacts, and the contribution of electrostatic interaction is seldom.
The molecular conformation for docking result is clustered, to be analyzed result and be compared, the cluster result such as institute of table 7
Show.
(unit is kcalmol to the cluster result of table 7-1)
Table 7 shows that Conjugated free energy is -7.47kcalmol-1Conformation 2 have most molecular conformation quantity, explanation
Manganese metal metalloporphyrin complex is most stable under the state of conformation 2.
Claims (10)
1. a kind of method that use computer simulation metal complex interacts with DNA, it is characterised in that including following step
Suddenly：
（1）The structure optimization of metal complex：In Gaussian softwares, mixed using the B3LYP functionals and use of DFT method
Base group, the metal complex structure to drafting carries out geometric hash, obtains the accurate structural of metal complex, structure optimization
Metal complex afterwards is used as ligand molecular；
（2）The structure of the region of search of ligand conformational：In AutoDock softwares, using DNA as acceptor molecule, to surround acceptor
Active binding site constitute lattice point box as the region of search of ligand conformational, and be that probe is carried out with different types of atom
Lattice point energy is scanned and calculates to calculate the interaction energy between probe atom and acceptor；
（3）Molecular docking：It is lattice point formula searching method with the AutoGrid subprograms in AutoDock softwares, in ligand conformational
Region of search search active binding site, make the molecular docking of acceptor and part；Finally metal complex and DNA are existed
Repeatedly docking is carried out in AutoDock subprograms to calculate and search for best combination position, and the docking result finally given is carried out
Analysis.
2. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（1）In, the metal complex for carrying out structure optimization is the metal complex in ground state.
3. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（1）In, in the use mixed base group, 6-31G** is used to the light atom including hydrogen, carbon, nitrogen and oxygen
Base group, heavy metal atom uses LanL2DZ base groups.
4. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（1）In, the metal complex after structure optimization saves as PDB formatted files.
5. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（2）In, the crystal structure of the DNA derives from the structure of the DNA in Protein Data Bank, and simulation process
The crystallization water and ion are deleted, the DNA crystal structures of acquisition do not include the coordinate data of hydrogen atom, add all hydrogen atoms.
6. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（2）In, the region of search of the ligand conformational includes whole DNA molecular structure, it is ensured that metal complex
It is be combined with each other with DNA any part.
7. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（2）In, in the region of search of the ligand conformational, lattice point at intervals of default value 0.0375nm.
8. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（2）In, the different types of atom includes tri- kinds of atoms of C, H and O；The calculating lattice point energy, mainly
Calculated by the AutoGrid subprograms in AutoDock softwares.
9. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, it is special
Levy and be, step（3）In, the computational methods of the docking are the Lamarckian genetic algorithm in AutoDock softwares.
10. the method that a kind of use computer simulation metal complex according to claim 1 interacts with DNA, its
It is characterised by, step（3）In, the docking operation is carried out under the K of default temperature 298.15.
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| CN109255427A (en) * | 2018-08-30 | 2019-01-22 | 无锡城市职业技术学院 | A kind of molecular docking calculation method based on quantum particle swarm optimization |
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