ReaxysTutorial. Dr. QF Carlos F. Lagos

Transcription

1 ReaxysTutorial Dr. QF Carlos F. Lagos

2 Agenda 1) Reaxys Basics Main Settings Query Menu: Reaction, Substances and Properties, Authors and citations Generate a structure t from a name Commercial Availability Tags 2) Reaxys Advanced Tips & Tricks Synthesis planner tool Find IC 50 for enzyme inhibitors Export Data and Citations Find Anti malarial Properties of Selected Natural Products

3 Structure Editors usable with Reaxys Reaxys uses ChemAxon s MarvinSketch as default structure and reaction query editor, if no other editor is selected. You can change your settings to use one of the following other editors: ChemAxon MarvinSketch CrossFire Structure Editor Symyx Draw Symyx ISIS Draw ChemDraw ICEdit Please note: You need to install the Reaxys Structure Editor Plug in (available at y g ( before you can use other editors)

4 Select Your Structure Editor in Reaxys 1 2 After installing your external structure editor, Reaxys Plug in, and any additional plugin that may be necessary...select your structure editor in Reaxys by doing the following: Click the My Settings button on the button bar Click the Modify Application Settings link 3 Select the structure editor by clicking a radio button. Then click the Save button at the bottom of your screen 1 2 3

5 Basic Compound and Filtering Search Techniques Find reactions to synthesize the drawn compound. Slide 5

6 The Search Progress box displays the progress of an active search as a percentage of the progress bar along with the number of hits retrieved. A search in progress can be stopped by clicking the Cancel button. Slide 6

7 Reactions are displayed in the Results menu (tabular views). Every reaction hitset is accompanied by a corresponding de-duplicated duplicated citation list. Reactions and Citation tabs are topped by the Breadcrumbs which keeps track of your result analysis. The hits are displayed in a tabular overview. Different conditions of the same reaction extracted from different publications are merged together in one tabular overview. Click the Show Details link to see the yield, conditions and the source Slide 7

8 Due to the variability in the conditions used, you need to focus on reactions done with a specific reagent or catalyst, and. Expand the Reagent/Catalyst filtering option by clicking the down arrow. Slide 8

9 Check the box close to Sulfuric acid. Click Limit to button. Slide 9

10 Basic Reaction Search Techniques Search reactions by drawing a reaction scheme This demo shows how to search the chemical reaction by drawing a reaction scheme (using ChemAxon Marvin SketchDirect as by drawing a reaction scheme (using ChemAxon Marvin Sketch Direct as structure editor)

11 Double click the structure box to launch the default structure editor. Slide 11

12 You will now use a query feature: a constraint to allow any type of substitution on specific atoms. Select the edit tool. Then, press the DOT key of your keyboard. Then, press the S key. Then, press the 6 key.

13 Notice the cursor

14 Press the arrow key and draw a reaction arrow on the screen.

15 Press the arrow key and draw a reaction arrow on the screen.

16 Click the Transfer button to bring back the reaction in Reaxys.

17 Your reaction will be searched As Drawn, with only substitutions allowed on selected positions. Slide 17

18 Click Search button. Slide 18

19 The reaction hitset is displayed in the Results window. Slide 19

20 As an alternative to drawing a structure, you can create a substance query by typing a substance name or other identifiers, such as CAS number or SMILES/InChI keys. Click the Substance and Properties Tab Slide 20

21 Click Generate Structure from name button Slide 21

22 Type in a chemical identifier (here the identifier: CHIR-258) Press Submit to call the structure. Slide 22

23 If multiple substances share the same name, you are presented with the list. Press Submit. Slide 23

24 The chemical structure is displayed in the structure box Slide 24

25 If needed, edit your chemical structure by double-clicking in the structure box Slide 25

26 Click the Search button to launch your search. Slide 26

27 The Search Progress box displays the progress of an active search as a percentage of the progress bar along with the number of hits retrieved. A Cancel button is visable before the search is complete. Clicking the Cancel button will stop the search without displaying the results. Slide 27

28 Substances are displayed in the Results menu (tabular views). Every substance hitset is accompanied by a corresponding de-duplicated citation list. Substances and Citation tabs are topped by the Breadcrumbs which keeps track of your result analysis. Slide 28 The tool bar gives access to the Limit to Selection, Output and Sort by tools features. The substances are by default sorted by descending No of References.

29 To see other articles, which cite this article click the link to switch over to Scopus

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31 Information linked to the commercial availability of compounds is available. Click on to link to the emolecules website, or on to link to the Symyx Available Chemicals Directory database. Slide 31

32 By clicking on you were linked to the emolecules website. Here you can view available Suppliers and prices. Slide 32

33 In the Available Data column, you may click on Identification, Physical Data, Spectra, Bioactivity/Ecotox, Use/Application to get additional information about the properties of the compound. Click on Physical Data to view measured experimental data of CHIR-258 Slide 33

34 Slide 34 The N of ref. column contains a link to the list of available references from patents and journals. Click on 15 to view the list of the 15 available literature references.

35 In the N of prep column, click on 6 (prep out of 11 reactions) to get information about all preparation reactions of CHIR-258. Slide 35

36 To find synthesis routes for a specific compound, click first the Reactions tab Slide If you know the chemical name, CAS-RegNo or InChi-Key of your product or a fragment of it click the Generate Structure from name button

37 Enter the chemical name or the CAS-Registry Number of your product, or a fragment of it. Or use SMILES Try this one: O=C(NC1=CC=CC=C1)C2=C3C(N=C(C4=NC=CC=C4)N3)=CC=C2

38 NO HITS!!!!!!!! Double click the frame and edit the query

39 By default, the entered structure will be searched with a role of Product; other roles can be assigned: Starting material, Any role, or Reagent/Catalyst. 2. The entered structure will be searched by default As Drawn (including possible query features added in your structure); but you can also launch a Substructure search. 3. If needed, additional query options and further search conditions like excluding salts, mixtures etc. can be added. 4. Click Search to launch your query.

40 Reactions are displayed in the Results menu (tabular views). Reactions and Citation tabs are topped by the Breadcrumbs which keeps track of your result analysis. Hits are displayed in a tabular overview showing the reaction scheme, the yields, conditions and the source Different conditions of the same reaction extracted from different sources (journal articles, patent publications) are merged together in one tabular overview.

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42 Export Enzyme and IC50 Data from a List of Patent Numbers I have a list of patent t numbers. I would like to retrieve all of the substances from those patents and then export any enzyme data along with IC50 values. There are 3 main ways to do this after first importing a list of patent numbers*. 1. Click the Output button. Next to Export Contains, click the Select Data radio button. Select Bioactivity data. The exported file contains all bioactivity data from all substances in the list. 2. Filter the list by specific bioactivity fields before clicking the Output button. Then select Hit Data Only in the Output box. Only substances with that data will be exported (if the list was filtered by multiple fields, the OR operator will be applied). 3. Perform an additional query to search Reaxys for IC50 data and enzyme data using the PROXIMITY operator so that both data points come from the same fact record. Click the History button, select both result lists, click the Combine button, and select the Overlap option. Export the newly-created list, selecting Hit Data Only from the Output box. Only substances with the desired data will be exported. *How to import a list of patent numbers Create a text file in NotePad using the following format: CIT.PN = ep ;ep ;wo2006/123113;us Then, click the Load Query/Batch button at the bottom of the Reaxys Query page, locate the text file and import it by clicking the Open button. This can be done from either of the 3 query tabs.

43 Retrieve a list of patents Load a batch file (Notepad txt file) from the Text, Authors, and More Tab. 26 citations, 691 compounds Start the search. Export Option #1 Export pharma data Select Data March 8, 2011 Slide 43 Retrieves all pharma data from the 691 compounds

44 Export Option #2 Export pharma data Select Hit Data Only Filter the list of patents All rows will have either Enzyme or IC50 (or both) March 8, 2011 Slide 44

45 1 Export Option #3 Perform an additional query Query Results 2 Select Overlap Click the History button, select the 2 entries, then click the Combine button 3 Select Hit Data Only March 8, 2011 Slide 45 The export file contains the desired information (in addition to other pharma fields and the reference field)

46 Find DNA Minor Groove Binders with Low IC50 Values I d like to find substances that have DNA minor groove binding affinity data. I d also like to know if any of these substances have been isolated from natural products. There are couple of different ways to approach this. The easiest would be to use the Substance Basic Index field and search for the phrase minor groove bind and then filter to isolate those with Natural a Product information o and IC50 data. a (Alternatively, e you can include Natural Product in the query). The Substance Basic Index field searches the substances data fields. You can also search the Citations Basic Index field for the phrase minor groove bind. This field searches the bibliographic fields. The IC50 data should be searched from the Pharmacological Data Type field and can also be found by filtering the results by the Bioactivity/Pharmacological Data/Type filter.

47 Substances and Properties Tab Substance Basic Index Use the Substance Basic Index field to search for text in all of the substance data fields (does not include the bibliographic fields). The NEXT operator ensures that the word groove will follow the word minor. The PROXIMITY operator ensures that the words will appear in the context of the same data. Click to view the index and select text

48 Example results: Results

49 Filter Results Filter the list by Natural Product to retrieve only substances with NP info (or to exclude them from the list)...

50 ...Or include the Natural Product field in the query Alternative Method Query Result example:

51 Query Citations Basic Index Text, Authors, and More tab. Search the bibliographic fields. Result example: Click to view substances in the article

52 Query Citations Basic Index & Pharmacological Type Result example: Include IC50 in the query Results can have different units nanomole micromole

53 Finding Specific IC50 Values IC50 lower than 1 nm IC50 data is usually found in the Type field along with the Value of Type field The units for the Value of Type field are not normalized. Therefore, you should try searching in a variety of ways (including converting nanomoles to micromoles).

54 Find Natural Products with Anti Malarial Activity New Caledonia is home to many plant species containing substances of medicinal value, including those on the following list. Is there any evidence of anti-malarial activity associated with these substances? Do these substances possess additional bioactivity? Genus Cunonia Dysoxylum Croton Garcinia Calophyllum Morinda

55 Query Search for anti-malarial substances isolated from these natural products Pharmacological effects = anti-malarial AND Natural Product March 8, = 2011 Cunonia;Dysoxylum; Croton;Garcinia;Calophyllum;Morinda Slide 55

56 View Details Retrieve a list of substances and view the Hit Data Hit data for each substance is labeled and stands out from the rest of the data. March 8, 2011 Slide 56

57 View Details Including info about the test method, dosing, abstract, and citing articles Biological Activity Citing Articles Abstract March 8, 2011 Slide 57

58 View Properties In addition to the Hit Data, additional properties show that this compound: Has antibacterial activity against staph aureus Has anti fungal activity Has NMR Data Has also been isolated from the bark of Allanblackia from Cameroon

59 Export Results

60 Thanks for your attention For more information visit iit REAXYS training center site center What s yourreaction! reaction!