Module II

Lead Identification

Assignment

You were requested as a computational biologist to identify leads against SARS CoV 2 the virus that is responsible for Covid 19. You were giving a heads up that chloroquine is presently been reported as a promising drug against the virus. You were requested to identify your leads using the ligand based design method:

  1. Using the PubChem database identify 20 possible leads against Covid 19 using the 2D fingerprint similarity search and download them in 3D SDF format.

  2. By increasing the Tanimoto Coefficient to 0.98, identify the best 5 leads.

  3. Using chloroquine as a pharmacophore, how many compounds had chloroquine as their pharmacophore.

  4. Using the Lipinski rule of five as a filter, how many compounds that have 2D similarity with chloroquine can be selected as leads.

  5. Using the 3D similarity screening method using the SwissSimilarity server, identify 15 leads that have similar 3D structure using the spectrophores similarity feature to search the Zinc database and FDA approved drugs.

  6. Using your result from question v. Predict their common target.

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