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opthitlead [2013/10/09 10:35]
rkiss
opthitlead [2014/01/01 16:51] (current)
flack
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 ====== Optimize hits and leads ====== ====== Optimize hits and leads ======
  
-[[http://youtu.be/Kb7HIPNpHzw|{{:hello.png?100|}}]] **[[http://youtu.be/Kb7HIPNpHzw|Check out how Ed, the chemist optimizes his identified hit using Mcule >>]]**+[[http://youtu.be/Kb7HIPNpHzw|{{:hello.png?100|}}]] **[[http://youtu.be/Kb7HIPNpHzw|Check out how Ed, the chemist optimizes his identified hit using Mcule »]]**
  
 Mcule offers a continuously growing set of intuitive, easy-to-use modeling applications specifically designed to evaluate and generate ideas in the hit/lead optimization process. Mcule offers a continuously growing set of intuitive, easy-to-use modeling applications specifically designed to evaluate and generate ideas in the hit/lead optimization process.
  
-**__[[usecase1cd|Optimize binding affinity and selectivity with 1-Click Docking >>]]__**+**__[[usecase1cd|Optimize binding affinity and selectivity with 1-Click Docking »]]__**
  
-**__[[usecase1csh|Generate new ideas and eliminate problematic parts by 1-Click Scaffold Hop >>]]__**+**__[[usecase1csh|Generate new ideas and eliminate problematic parts by 1-Click Scaffold Hop »]]__**
  
-**__[[usecasepropcalc|Property calculator >>]]__**+**__[[usecasepropcalc|Property calculator »]]__**
  
-**__[[usecasetoxcheck|Toxicity checker >>]]__**+**__[[usecasetoxcheck|Toxicity checker »]]__**
  
 -- --
  
-**__[[usecases|Go back to use cases >>]]__**+**__[[usecases|Go back to use cases »]]__**
  
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-====== Property calculator ====== 
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-ADMET properties heavily depend on physicochemical properties. For example, high logP (> 5) and molecular weight (> 500 g/mol) are typically associated with unsuitable ADMET profile. Property calculator creates a physicochemical property profile for your compound in seconds. You can reject compounds with unsuitable logP, insufficient number of H-bond acceptors/donors, too many rotatable bonds, etc. 
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-1. Go to **[[http://mcule.com/apps/property-calculator|LEAD OPTIMIZATION / PROPERTY CALCULATOR]]** 
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-2. Specify your existing hit/lead (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) 
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-3. Click on **"CALCULATE"** 
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-4. Check the calculated properties of your original hit/lead. Depending on your **[[http://mcule.com/pricing|Price Plan]]**, you might see **Basic** as well as **Advanced** properties. Notice if there are properties in unsuitable/unacceptable ranges (e.g. too high logP). 
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-5. Go back and draw a slightly modified version of your hit/lead 
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-6. Click on **"CALCULATE"** 
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-7. After the calculation finishes you can check the individual properties and see if problematic properties got improved due to your modification in the hit/lead structure 
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-8. You can use the other Lead Optimization tools, such as **[[http://mcule.com/apps/1-click-docking|1-Click Docking]]** and **[[http://mcule.com/apps/toxicity-checker|Toxicity Checker]]** to make sure other properties of the ligand are not impaired. In fact, try to improve multiple things simultaneously by checking all properties of the same idea. 
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-**__[[usecases|Go back to use cases >>]]__** 
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-====== Toxicity checker ====== 
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-Certain structural elements of a molecule can be responsible for toxicity. In fact, some substructural motifs occur more frequently in toxic compounds than in non-toxic ones. It therefore makes sense to eliminate such structural motifs from hits/leads as early as possible. Toxicity Checker is based on more than 100 toxic and promiscuous scaffolds. It displays an alert, when such a motif is found, and it displays the incriminated part of the molecule. 
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-1. Go to **[[http://mcule.com/apps/toxicity-checker|LEAD OPTIMIZATION / TOXICITY CHECKER]]** 
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-2. Specify your existing hit/lead (either by drawing or by providing a chemical identifier such as mcule ID, SMILES, InChI or InChIKey) 
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-3. Click on **"CHECK"** 
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-4. If the compound contains any potential toxic substructure, **"FAIL"** message will be displayed along with your structure and the problematic motif in red 
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-5. Go back and try to modify the problematic motif of your hit/lead 
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-6. Click on **"CHECK"** 
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-7. Continue the modifications, until no alert is displayed 
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-8. You can use the other Lead Optimization tools, such as **[[http://mcule.com/apps/1-click-docking|1-Click Docking]]** and **[[http://mcule.com/apps/property-calculator|Property Calculator]]** to make sure other properties of the ligand are not impaired. In fact, try to improve multiple things simultaneously by checking all properties of the same idea. 
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-**__[[usecases|Go back to use cases >>]]__** 
opthitlead.1381307752.txt.gz · Last modified: 2013/10/09 10:35 by rkiss