CN106156405A - Organic synthetic route design method based on chemical reaction data storehouse - Google Patents
Organic synthetic route design method based on chemical reaction data storehouse Download PDFInfo
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Abstract
The present invention relates to a kind of method for building up and the organic synthetic route design method based on described chemical reaction data storehouse in chemical reaction data storehouse, described chemical reaction data storehouse has considered not only reaction site in the algorithm extracting reaction fingerprint, also fully take into account the compatibility of group in the impact of reaction site surrounding chemical environment and reaction, and the foundation of described chemical reaction data storehouse has been additionally contemplates that the cost factor of reactant feed, contribute to user to carry out based on above-mentioned database avoiding a large amount of irrational synthetic route branch during the Design of Organic Synthesis of target compound molecule, obtain limited amount and rationally, practicable synthetic route result.
Description
Technical field
The present invention relates to area of computer aided compound molecule design field, be specifically related to a kind of based on chemical reaction number
According to organic synthetic route design method.
Background technology
In field of fine chemical such as new material, pharmacy, agricultural sciences, skin care item, it is frequently necessary in R & D of complex
Go to synthesize each organic molecular species.In order to be able to obtain the target molecule needing, or in order to reach to optimize production line, reduce cost
Etc. purpose, need to carry out the design of organic synthesis route for target molecule.Organic synthetic route design difficulty is very big, has in the past
The design of machine synthetic route relies primarily on the research and development technology personnel knowledge and experience of self.But with sending out of current information technology
Exhibition, with the foundation of database of the organic synthesis knowledge of ever-increasing magnanimity, research and development technology personnel can be by database
Carrying out inquiring about the synthetic method understanding target molecule or its similar molecules, chemical knowledge and experience then in conjunction with oneself are carried out
Synthetic route designs, and can greatly reduce workload and the working time of person skilled, effectively improve the efficiency of synthetic work.
The software of the computer assisted organic sythesis highway route design occurring in the market, its general principle is first according to a large amount of chemical reactions
Data extract the part (referred to as reaction center) changing in reaction, and the target molecule that then will synthesize and reaction center are entered
Row coupling, then backstepping reactant until the chemicals raw material that is commercially available, thus obtains the complete of synthesis target molecule step by step
It is integrated into reaction scheme.But above computer Autocad is only basic as coupling using reaction center, and operand is big, each
Step reaction all can have tens or even hundreds of different possibility, and the operand exponentially rank of whole process increases, and can cause fortune
Evaluation time is long is even difficult to inquiry, and the chemical bond that do not considers in chemical reaction in addition to reaction center, atom, group also may be used
Can affect process and the result of reaction, often obtain substantial amounts of unreasonable route, still need to technical staff and utilize experience and knowledge
Enter row filter, it is also possible to the experimental work amount that some are unnecessary and economic loss can be caused.
Patent CN201010106648.9 discloses a kind of organic micromolecule compound based on reverse reaction can be synthetic
Evaluation method, described method includes: set up raw database, transformation rule database and route database, apply this three
Individual database carries out reverse reaction analysis to target compound, automatically generates the synthetic route of organic micromolecule compound, is tearing open
During Fen, the generation to reverse reaction parsing tree is optimized process, deletes the node in reverse reaction parsing tree in advance, closes
Become after Route Generation, difficulty is evaluated to be realized to the fractionation difficulty of compound and synthetic route simultaneously.This patent is considered
The impact of reaction center surrounding chemical environment, when extracting reaction center, identify after reaction site by with in reaction site
The functional group that atom is connected also extracts, and has carried out the abstract of reaction center, but does not takes into full account surrounding chemical environment
Surrounding chemical environment is simultaneously effectively treated by concrete impact accordingly, and meanwhile, this patent only considered from target molecule to raw material
The derivation of molecular orientation, does not carry out the pre-derivation to the more complicated molecule synthesizing from raw molecule one end, not by former yet
Material price factor is taken into account, still may produce when utilizing its database to inquire about and design and substantial amounts of not conform to line of reasoning
Line, is even difficult to find that rational route owing to operand is excessive.
Content of the invention
For overcoming the deficiencies in the prior art, the present invention provides the method for building up in a kind of chemical reaction data storehouse, including as follows
Step:
(1), after chemical reaction data being converted to Computer Storage form, carry out processing acquisition reactant and product Central Plains
The one_to_one corresponding information of son；
(2) corresponding informance according to step (1), identify reaction site, and by reaction site and with reaction site direct phase
Company, the atom of phase conjugate, chemical bond, group and be indirectly connected to reaction site and affect the group of reaction as identifying that chemistry is anti-
The information answered extracts, and is saved in database as reaction fingerprint；
(3) corresponding informance obtaining according to step (1), it is judged that in reaction, group to the compatibility of reaction condition and will determine that
Result is saved in database, and in chemical reaction, the group all existing in reactant and product for described reaction condition is
Compatible, exist in reactant but non-existent group is incompatible for described reaction condition in the product.
Chemical reaction described in step (1) include conventional chemical reaction, classical organic name reaction, published other
Chemical reaction, the chemical reaction as reported in academic journal or patent；The reaction condition of described chemical reaction, product divide
From purification process, reaction yield etc., for information about and bibliography is also saved in database with realization reaction；
Preferably, the process described in step (1) includes that the chemical constitution by the reactant in chemical reaction and product is built
Vertical mapping relations (mapping computing)；
Preferably, the process described in step (1) also includes: removes and does not affects reactant and product chemistry in chemical reaction
The hydrogen atom of representation, by aromatic rings in reactant and product with the chemical bond that Kekulé formula represents be converted to identical from
Territory big π key, single double bond of aromatic rings will be converted to unified aromatic gp；
The Computer Storage form of molecular structure of compounds is more, such as MOL2, MOL, SDF, MOP, ALC, SMD, RDF etc.,
Those skilled in the art can carry out the selection of above-mentioned form according to actual conditions, and this is not construed as limiting by the present invention；
Reaction site described in step (2) includes atom and/or the chemical bond participating in chemical reaction, including from reactant
The atom, chemical bond and the atom that be added in the change of product, change, disappear and the combination of chemical bond；
Preferably, the reaction fingerprint described in step (2) includes: participates in the chemical bond of chemical reaction, participate in chemical reaction
Atom and the chemical bond of atom phase conjugate of the atom that is joined directly together of atom of participation chemical reaction and participation chemical reaction
And atom and participate in the atom of chemical reaction or electron withdraw group that the chemical bond being conjugated therewith is joined directly together and donor residues
What group, the atom with participation reaction were directly or indirectly connected has sterically hindered group；
The compatibility determination result of group is contributed to predicting in reactant whether contain according to reaction condition by step (3)
There is incompatible group, and carry out rejecting and the optimization of related synthetic route accordingly, it is to avoid cause failure and the damage of synthetic reaction
Lose；
Preferably, described method for building up also includes existing compound products as raw materials of compound, sets up chemical combination
Raw material database, is stored in above-mentioned chemical reaction data storehouse；Described existing compound products is can in prior art
The compound products directly being bought by commercial channel；It is further preferred that above-claimed cpd raw database also includes
The price of raw materials of compound, the information such as No. CAS；
Preferably, the reaction fingerprint that can obtain according to step (2) sets up reaction fingerprint database, is stored in above-mentioned chemistry anti-
Answer in database；
Preferably, the group compatibility determination result that can obtain according to step (3) sets up group compatibility analysis database,
It is stored in above-mentioned chemical reaction data storehouse；
Preferably, the chemical reaction according to step (1), the product of collection chemical reaction, as the compound that can synthesize, is built
Vertical compound intermediate database, is stored in above-mentioned chemical reaction data storehouse；Described compound intermediate is with existing
Compound products is as the chemical combination by the chemical reactive synthesis in the above step of one-step or two-step (1) for the raw materials of compound
Thing.
The present invention also provides the chemical reaction data storehouse that a kind of said method is set up.
Preferably, described chemistry reflection database includes: raw materials of compound database, reaction fingerprint database, group
Compatibility analysis database；It is further preferred that also include compound intermediate database.
The present invention also provides a kind of organic synthetic route design method based on above-mentioned chemical reaction data storehouse, including as follows
Step:
(1) target compound is inputted；
(2) target compound is mated the chemical reaction product in above-mentioned database, the chemical reaction of coupling is output as
Accurate lookup result；
(3) target compound is mated the reaction fingerprint in above-mentioned database, obtain corresponding reaction fingerprint, reverse operation
Obtain the reactant of synthesising target compound, the chemical reaction of the respective reaction fingerprint of coupling is output as similar lookup result；
Preferably, (4) accurate lookup result described in step (2) respectively and the approximation lookup result described in step (3)
It is ranked up；
Preferably, the foundation of above-mentioned sequence includes needed for reaction yield, the compatibility of group, synthesising target compound
Number of reaction stages and reactant cost；Preferably reaction yield is high, without incompatibility group, synthesising target compound required reaction step
Suddenly less, the result of reactant low cost；Above-mentioned sort by may also include reaction condition and realizes that complexity, product separate and pure
Change difficulty, reactant toxic etc.；
The general principle of described target compound coupling is as follows: the structural formula of target compound is decomposed into multiple structure
Fingerprint, each fingerprint is represented by 0 and 1, as comprised three-membered ring, having the fingerprint definition such as oxygen atom, the chemical constitution of each compound
Can define according to fingerprint and be calculated as a binary digit, after defining enough fingerprints, binary digital according to this
Whether bit manipulation, can comprise another chemical constitution (superstructure) or by another with one chemical constitution of Rapid matching
Individual chemical constitution comprises (substructure) or essentially equal (exact), for inclusion relation, must arrive Rapid matching
Two structures carry out man-to-man structure matching again, remove the result that minority does not corresponds.Other can realize structural formula of compound
The method joined is also applied for the organic synthetic route design method of the present invention, and this is not construed as limiting by the present invention.
Reverse operation described in step (3) is according to reaction fingerprint, by corresponding atom and the chemical bond of target compound
Carrying out transformation by reciprocal direction, the reactant needed for synthesising target compound is progressively derived in the back reaction direction chemically reacted；Described
Reactant can be one or more compounds；Described reverse operation is more than one-step or two-step；
Preferably, the screening described in step (3) includes: removes the reaction containing unreasonable chemical constitution, produce accessory substance
The synthetic route of reaction；It is anti-that the reaction of described unreasonable chemical constitution includes that reactant instability or can not exist etc.
Should, whether whether the reaction of described generation accessory substance can be unique according to reaction site or selective judge；
Preferably, in step (2) and (3), from the beginning of target compound, after mating each time, provide after sequence
Join result selective, after selecting, enter next step inquiry and coupling, until completing the design of whole synthetic route；Described
Selection includes that user selects and give tacit consent to selection, and the matching result of sequence can arbitrarily be selected by user；As no user selects, then
Carrying out acquiescence to select, acquiescence selects successively to select according to sequence, preferably first result；User also can input one
It thinks that rational result carries out next step inquiry and coupling.
The chemical reaction data storehouse that the present invention provides has considered not only reaction site in the algorithm extracting reaction fingerprint,
Also fully take into account the compatibility of group in the impact of reaction site surrounding chemical environment and reaction, contribute to user based on above-mentioned
Database carries out avoiding a large amount of irrational synthetic route branch during the Design of Organic Synthesis of target compound molecule, is counted
Measure limited and rational synthetic route result；Described chemical reaction data storehouse includes commercially available compound products and valency thereof
Lattice, the information such as No. CAS, when carrying out organic synthetic route design based on described chemical reaction data storehouse in view of synthesis cost because of
Element, contributes to obtaining practicable synthetic route result；Above-mentioned Design of Organic Synthesis method is divided into when match query accurately
Search and approximation is searched, contribute to user and distinguish the synthetic route of existing synthetic route and design；And user may participate in selection often
The design of the synthetic route of one step, it is to avoid unreasonable synthetic route branch produces, and can obtain meeting the result of user's request.
Detailed description of the invention
Heretofore described " target compound " is the compound that user wants synthesis, and it can be deposited in prior art
Compound, as in certain pharmaceutical intermediate or drug design to certain molecule filtering out in known compound storehouse, also
Non-existent virtual compound in prior art can be, such as certain derivative with bioactive molecule or virtual chemical combination
Thing storehouse is deemed likely to have bioactive molecule.
Technical scheme in the embodiment of the present invention will be clearly and completely described below, it is clear that described enforcement
Example is only a part of embodiment of the present invention, rather than whole embodiments.Based on the embodiment in the present invention, this area is common
The every other embodiment that technical staff is obtained under the premise of not making creative work, broadly falls into the model of present invention protection
Enclose.
Embodiment 1 chemical reaction data process
Chemical reaction as shown in formula (1) is exported as RDF standard chemical data form.Wherein, atom is represented as joint
Putting and numbering, interatomic chemical bond is expressed as internodal connection, sets up mapping pass to the chemical constitution of reactant and product
System, removes the hydrogen atom not affecting reactant and product chemistry representation, the Dan Shuanjian of aromatic rings is converted to unified virtue
Fragrant key, it is thus achieved that the one_to_one corresponding information of atom in reactant and product, as shown in formula (2).Identify reaction site, extract reaction position
The chemical bond of point and the atom being joined directly together with reaction site and phase conjugate is as shown in reaction fingerprint such as formula (3).
Embodiment 2-in-1 one-tenth BOC-L-proline
Based on chemical reaction data library inquiry and the synthetic route designing BOC-L-proline of the present invention, accurately search and return
Returning 13 results and being sorted, wherein Article 1 result is for being synthesized BOC-L-dried meat ammonia by BOC acid anhydrides and L-PROLINE
Acid, two kinds of raw materials all directly can be bought by commercial channel, as follows:
Embodiment 3 synthetic drug valaciclovir
Based on chemical reaction data library inquiry and the synthetic route designing medicine valaciclovir of the present invention, accurately search and do not have
Have and obtain result, but through similar lookup, obtaining can be by two commercially available raw materials through single step reaction synthesising target compound
Route, as follows:
Embodiment 4 synthesizes 3-quinoline-6-base-propionic aldehyde
Chemical reaction data library inquiry and design 3-quinoline-6-base-propionic aldehyde (3-quinolin-6-based on the present invention
Yl-propionaldehyde) synthetic route, accurate lookup does not obtain result, but through similar lookup, and obtaining can be by
Two commercially available raw materials are through the route of single step reaction synthesising target compound, as follows:
Embodiment 5 synthesizes 7-benzyl-3,7-diazabicyclo [3.3.1] nonane-3-carboxylic acid tert-butyl ester
Based on the present invention chemical reaction data library inquiry and design 7-benzyl-3,7-diazabicyclo [3.3.1] nonane-
The synthetic route of 3-carboxylic acid tert-butyl ester, searches through accurate, obtains to be carried out through two-step reaction by two commercially available raw materials
The route of synthesising target compound, as follows:
In inquiry described in embodiment 2-5 and design result, synthetic route is shorter, and productivity is higher, synthesising target compound
Required reactant all directly can be bought by commercial channel, can greatly reduce the workload of technical staff, when shortening work
Between, effectively improve operating efficiency.
Embodiment 6 synthesizes compound 3-{3-[3-methyl-5-(propyl-2-yl)-4H-1,2,4-triazole-4-yl]-8-azepine
Bicyclic [3.2.1] octyl-8-yl }-1-phenyl propyl-1-alcohol
Utilize ChemPlanner (John Wiley&Sons company) to carry out the synthetic route design of target compound, obtain
As follows through the route of three-step reaction synthesising target compound by commercial compound raw material:
Based on the synthetic route of the chemical reaction data library inquiry of the present invention and design object compound, the lookup obtaining is tied
After fruit is sorted, Article 1 result is as follows through the route of two-step reaction synthesising target compound by commercial compound raw material:
Above two synthetic route is compared, and latter reaction's step is less, can reduce the conjunction of target compound greatly
Become cost and time.
Embodiment 7 synthesizes 2-[(quinolyl-4) amino] acetamide
Utilize ChemPlanner to carry out the synthetic route design of target compound, obtain by 4-halogenated quinoline and glycyl
Amine is as follows through the route of single step reaction synthesising target compound:
Based on the synthetic route of the chemical reaction data library inquiry of the present invention and design object compound, the lookup obtaining
After sort result, Article 1 result for by 4-oxyquinoline and glycine amide through the route of single step reaction synthesising target compound
As follows:
The chemical reaction data storehouse of the present invention contains the price price of raw materials of compound, the information such as No. CAS, based on this
When the chemical reaction data library inquiry of invention and the synthetic route of design object compound, the foundation that lookup result is ranked up
Including the compatibility of reaction yield, group, reactant cost etc., the compatibility for reaction yield, group is same or like, anti-
Answer the lookup result that step is identical, the synthetic route being of relatively low cost is come before.
The 4-oxyquinoline preserving in chemical reaction data storehouse according to the present invention and the price of 4-halogenated quinoline, the former
Price is significantly less than the latter's, is respectively adopted 4-oxyquinoline and the route reaction of 4-halogenated quinoline synthesising target compound is received
Rate, group compatibility are similar, and reactions steps is all a step, therefore will use the route row of 4-oxyquinoline synthesising target compound
In Article 1, the low cost of the synthetic route that its synthesis cost Billy designs with ChemPlanner much, thus actual can
OK.
The foregoing is only presently preferred embodiments of the present invention, not in order to limit the present invention, all essences in the present invention
Within god and principle, any modification of being made, equivalent etc., should be included within the scope of the present invention.
Claims (10)
1. the method for building up in chemical reaction data storehouse, comprises the steps:
(1), after chemical reaction data being converted to Computer Storage form, carry out processing atom in acquisition reactant and product
One_to_one corresponding information；
(2) corresponding informance according to step (1), identify reaction site, and be joined directly together by reaction site and with reaction site, phase
The atom of conjugation, chemical bond, group and be indirectly connected to reaction site and affect the group of reaction as identifying chemical reaction
Information extracts, and is saved in database as reaction fingerprint；
(3) corresponding informance obtaining according to step (1), it is judged that in reaction, group to the compatibility of reaction condition and will determine that result
Being saved in database, in chemical reaction, the group all existing in reactant and product is compatible for described reaction condition
, in reactant exist but in the product non-existent group be incompatible for described reaction condition.
2. method for building up as claimed in claim 1, it is characterised in that the process described in step (1) includes: by chemical reaction
In reactant and the chemical constitution of product set up mapping relations；And/or, removing does not affects reactant and product in chemical reaction
The hydrogen atom of representation；And/or, aromatic rings in reactant and product will be converted to phase with the chemical bond that Kekulé formula represents
Same delocalization big π key.
3. method for building up as claimed in claim 1, it is characterised in that the reaction fingerprint described in step (2) includes: participationization
The atom that is joined directly together of atom of the chemical bond learning reaction, the atom participating in chemical reaction and participation chemical reaction and participationization
Learn the chemical bond of the atom phase conjugate of reaction and the atom of atom and participation chemical reaction or the direct phase of the chemical bond being conjugated therewith
What the atom with electron donating group, with participation reaction for the electron withdraw group even was directly or indirectly connected has sterically hindered group.
4. method for building up as claimed in claim 1, it is characterised in that described method for building up also includes: by existing chemical combination
Produce product, as raw materials of compound, set up raw materials of compound database, are stored in described chemical reaction data storehouse；And/or,
Set up reaction fingerprint database according to the reaction fingerprint that step (2) obtains, be stored in described chemical reaction data storehouse；
And/or,
Set up group compatibility analysis database according to the group compatibility determination result that step (3) obtains, be stored in describedization
Learn in reaction database；And/or,
According to the chemical reaction of step (1), collect the product of described chemical reaction, set up compound intermediate database, store
In described chemical reaction data storehouse.
5. the chemical reaction data storehouse set up by the method for building up described in any one of claim 1-4.
6. the organic synthetic route design method based on the chemical reaction data storehouse described in claim 5, including walk as follows
Rapid:
(1) target compound is inputted；
(2) target compound is mated the chemical reaction product in described database, the chemical reaction of coupling is output as accurately
Lookup result；
(3) target compound mating the reaction fingerprint in described database, obtaining corresponding reaction fingerprint, reverse operation obtains
The chemical reaction of coupling respective reaction fingerprint is output as similar lookup result by the reactant of synthesising target compound.
7. method for designing as claimed in claim 6, it is characterised in that the reverse operation described in step (3) is for according to reaction
Corresponding atom and the chemical bond of target compound are carried out transformation by reciprocal direction by fingerprint, and the back reaction direction chemically reacted progressively pushes away
Derive the reactant needed for synthesising target compound；And/or,
Screening described in step (3) includes: remove the reaction containing unreasonable chemical constitution, the synthesis producing the reaction of accessory substance
Route.
8. method for designing as claimed in claim 6, it is characterised in that described method for designing also includes step (4): right respectively
Accurate lookup result described in step (2) and the approximation lookup result described in step (3) are ranked up.
9. method for designing as claimed in claim 8, it is characterised in that the foundation of described sequence includes: reaction yield, group
Compatibility, the number of reaction stages needed for synthesising target compound and reactant cost.
10. method for designing as claimed in claim 9, it is characterised in that in described step (2) and (3), from target compound
Start, each time mate after, provide sequence after matching result selective, enter after selecting next step inquiry and
Join, until completing the design of whole synthetic route.
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| CN111429976A (en) * | 2020-03-24 | 2020-07-17 | 上海交通大学 | Optimized screening system and method for reaction flux for directionally removing impurities in molten metal |
| CN111951905A (en) * | 2020-08-14 | 2020-11-17 | 中国科学技术大学 | Chemical reaction searching method and system |
| CN112133379A (en) * | 2020-09-18 | 2020-12-25 | 武汉智化科技有限公司 | Chemical reaction search method, device and system and graphic processor |
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| CN112272764A (en) * | 2018-01-30 | 2021-01-26 | 斯坦福国际研究院 | Computational generation of chemical synthetic routes and methods |
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| CN111951905A (en) * | 2020-08-14 | 2020-11-17 | 中国科学技术大学 | Chemical reaction searching method and system |
| CN112133379A (en) * | 2020-09-18 | 2020-12-25 | 武汉智化科技有限公司 | Chemical reaction search method, device and system and graphic processor |
| CN114388071A (en) * | 2021-12-31 | 2022-04-22 | 明度智云(浙江)科技有限公司 | Method and device for managing compound synthesis path and storage medium |
| CN116386753A (en) * | 2023-06-07 | 2023-07-04 | 烟台国工智能科技有限公司 | Reverse synthesis reaction template applicability filtering method |
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