Introduction to Spark
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- Wilfrid Johnson
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2 As you become familiar or continue to explore the Cresset technology and software applications, we encourage you to look through the user manual. This is accessible from the Help menu. However, don t waste time contact us if you have any questions or need help. These discussions, and the process of helping our customers, provide insight for how we can improve our science and user experience. Contact us via phone or . 2
3 In this first section, we will briefly discuss the science underpinning all of Cresset s software. 3
4 The 2D drawing of a molecule gives limited information about its nature in real life, molecules take on a 3D geometry whose nature can t be truly represented by a flat cartoon. Consider the electrostatic potential surrounding a molecule and map that potential out to a surface as shown in the second figure. Field points are points that are placed at the extrema of the MEP, with the point size governed by the size of the electrostatic contribution. Spatial points are also included at the van der Walls radii extrema. We use these field points to guide how we align and assess how similar molecules are. 4
5 Underlying all of Cresset s software is our XED forcefield. The extended Electron Distribution forcefield differs from traditional molecular mechanics force fields in the sense that we have included p orbital electrons with their own optimizable parameters (charge, bond lengths/angles/dihedrals) that are included in the minimizations. This allows us to split the charge and put the positive charges on the nucleus and the negative charges out in the 'cloud', which is what we would expect for an atom. This means that we get electrostatically driven interactions like π π stacking correct, as well as have a representation of electrostatics that is more in keeping with what is seen experimentally If you look at the substitution of the benzene ring with halogens, you can see the electrostatics of the π cloud changing. As you go down the group, the groups become more σ donating. 5
6 Using a 3D electrostatics and shape based alignment can allow the comparison of structurally diverse molecules and reduce reliance on having a common scaffold. In essence, we are comparing molecules in the true sense of bioisosterism. In the picture, we see that three structurally very different molecules have very similar field point patterns in their bioactive conformations. 6
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8 With Spark, we include a database of fragments which are used for bioisosteric replacement experiments. Common experiments include scaffold hopping or core replacement, R group replacements using available reagents, fragment growing. Using the Spark software, you can increase the novelty of your modifications, fill in gaps in patents (patent bust), assess available chemistry space, and finally, at the end of the project, protect your patent by ensuring bioisosteric analogues are also covered. 8
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12 Spark uses a product centric approach, that is all potential bioisosteres are scored only as complete product molecules and not as isolated fragments. To create the products with suitable properties a multi stage process is used. Once you have chosen the portion of the target molecule that you wish to replace, a copy of the target is created with these atoms removed. The geometric distance and angles between any broken bonds are recorded. Spark then searches a database for any fragment that has the right number of connection points that geometrically match the broken bonds in the target. Matches are considered on the basis of both angle and distance. 12
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15 Fragments that have the correct angles and distances between connection points are merged into the target molecule to form the 'product'. Only now, as a whole product molecule is this bioisosteric replacement scored against the starting structure for electrostatic and shape similarity. Using this product centric view generates a wider range of biologically relevant bioisosteres. 15
16 Spark s product centric approach gives excellent results, producing a more diverse set of bioisosteres. The graphic shows an overlay of the thiazolotriazine (bottom right, grey carbons) with rofecoxib (green carbons). The Field pattern surrounding the retained portions of the molecule are highly conserved in these molecules (both are active), however, subtle changes can still be seen particularly near the sulfone group. 16
17 The Spark fragment databases come from a number of sources, including both literature and commercially available compounds that have been fragmented, and conformationally populated. The fragment databases are organized based on the frequency of the fragment occurrence for example, the VeryCommon fragments have been seen more than 400 times. We believe that there is a correlation between fragment frequency and synthetic accessibility, especially for the fragments derived from commercially available compounds. Very common fragments are generally well explored and easy to make; on the other hand, the Very Rare fragments are rare because they are either difficult to synthesize, or are exceptionally novel! The Reagents databases are built up by fragmenting commercially available emolecules libraries in a chemistry sensible way to give fragment databases that are R groups. These collections can allow you to exploit a specific synthetic scheme, and have availability information available for the reagents of interest. There is also an optional module which can be used to create fragment databases from internal collections. 17
18 If you are working along with me and do not have the files shown above, please ask! In this section, we will take the ligand from the 1oit crystal structure and do an R group replacement using Spark. For this section, that file is called spark_1oit_results.fsp. In that file, we ve picked a few of our favorites which you are welcome to explore and select additional modifications that you like. 18
19 Double click on the Spark icon to launch the Spark software. You will notice that Spark, like all of the Cresset software, is driven by a wizard that will take you through the process of setting up experiments. Click 'New Project'. 19
20 In Spark, you have the option to work outside of the wizard by choosing 'Blank Project'. Alternatively, you can open an existing project, search for bioisosteric replacements, update databases, or generate fragment databases. Click 'Search for Bioisosteric Replacements'. Notes: Update Databases requires an internet connection and allows you to download updates. Generate Fragment Database requires an optional license, which allows creation of new fragment databases from company inventory systems, registration systems, etc. 20
21 In the first set up panel, you are asked to load a starter molecule. The starter molecule is the molecule which you want to make changes to. If you do a basic experiment, you can score the new molecules back to the starter. The other option is that you bring in multiple molecules to be used in the scoring. One of those molecules will be the starter (i.e., the one you make changes to), while the others will be references and used for scoring. For this experiment, we will start from a protein pdb file and extract the lead for Spark from the file. The pdb ligand will be the starter, and the reference for scoring. Click Protein and browse for and open the 1OIT.pdb file If you have an internet connection, you can grab pdb files directly from the RCSB. 21
22 In this next panel, you have the option to choose how protonation state is determined. If you choose to use the input protonation state, the protonation state will be determined based on the data in the PDB file so all charged residues are likely to come out neutral. If you choose to let 'Spark choose the protonation state', a set of rules will be applied to determine the charging, which gets the obvious cases of protonated amines and deprotonated carboxylates. This is reliable for protein residues but it is always worthwhile to check the protonation state of the ligands when you bring them in as a researcher working on specific problems, you know what the protonation state should be. For this example, choose 'Let Spark choose the protonation state' and click 'Open'. 22
23 The protein import window shows a 3D view and a hierarchy view of the PDB file. Chains can be expanded or collapsed. The table can be sorted on any column. Selecting an item in the table also selects it in the 3D window. The intention of this window is to make it easy to find and split out your ligand from the protein. Spark uses ligand similarity to assess suggestions with the protein only used as a region of excluded volume. As such it is normal to reduce the protein structure to just the atoms that you know do not move. In practice this means deleting the water molecules and occasionally removing loops. In this experiment the 1OIT structure has only a single chain with a single ligand. We choose the ligand as our starter molecule by selecting it and clicking Use as Reference. We Delete Waters and import the remaining atoms as an excluded region with the Import as Protein button 23
24 If starter and other references are used, there is a toggle to select the starter, as well as fields where the scoring weight can be modified. With a starter that will also be the sole reference for scoring. It is worth checking that the 2D structure and bonding match your expectations. PDB files occasionally get the bonding wrong. If you need to make changes then the Edit link will open the 3D editor. No changes are necessary here. Click Next. Page 24
25 In this panel, select the region of the starter molecule that is to be replaced, as shown, by left dragging a lasso. Click Next. Page 25
26 In this panel, you have the option to select what atom types you are willing to accept in any fragments that will be considered as a replacement. For this experiment, we will not make any restrictions here, but rather use a chemistry aware fragment database. Click Next. 26
27 This panel enables the separate loading of a protein excluded volume. We have an option to clear it and load an alternative but that is not necessary for this experiment Click Finish Page 27
28 The next part of the Spark experiment is to select which fragment databases will be searched. For this experiment, we want to exploit a particular synthetic chemistry motif, so the Cresset Reagents fragments will be used, specifically the Boronic acid fragments. This is a small database of 9,487 fragments. With such a small search space the results may be limited in novelty. We could expand the results later with additional databases such as the emolecule_aromatic_halide database. The Cresset Reagents fragment databases are a repackaging of the commercially available emolecules database in a way that is chemistry aware, and can be used to find replacements that will cooperate with the chemistry you are planning to do. Choose emolecule_boronic. The Show Options button gives access to all the parameters available for the search but the default Normal conditions work well in most cases. Click Start. Page 28
29 This calculation takes 4 or 5 minutes to complete. If yours is progressing through the stages well then feel free to wait If your experiment is progressing slowly then you can load the results from a project file. Click Cancel to stop the calculation then Open and choose the spark_1oit_results file. Page 29
30 Once the calculation completes, the results will be shown in the Results tables. The Standard Results table shows individual results, sorted on score. The Clustered Results table shows the results sorted into chemical families with a parent molecule chosen and displayed for each family. The Tile Results table shows a MedChem friendly view on the results. Take a few minutes and explore the three tables and understand the different view on the same information. 30
31 Any result in Spark can be marked as a Favorite. Favorites can be exported, copied, printed or displayed independently of other results. You can mark a result as a Favorite by clicking on the star in the below the 3D window or by pressing the space bar. Browse the results and select 5 favorite results. You can display just the favorites in the 3D view by turning Sel off and turning Fav on, on the righthand button bar. You can also tag results by using the right-click menu from the Results Tables. 31
32 The way molecules are displayed in the 3D window is controlled by the toolbar at the top of the application. Critical to understanding this toolbar is the drop down chooser that controls the which molecules will have their display style changed. Selected Molecules changes just the molecules that you currently have selected Reference and Results changes all the ligands in the project Protein changes just the protein useful for changing color or applying a molecular surface 32
33 Render the electrostatic surfaces for the reference and the favorite ligands. It is helpful to look at the ligands separated from the reference and in Grid mode. Note the similarities to and differences from the reference, which is circled. Some of these favorites look ok, while others look like they could use some work. 33
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35 As you become familiar with Cresset s technology and software applications, we encourage you to look through our user manual, which is accessible from the Help menu. But of course, we d much prefer that you contact us should you have any questions or need help. Often time, these discussions and the process of helping our customers provide us with insight for how we can improve our science and user experience. Please don t hesitate to contact us via phone or . 35
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