Pharmacophore-based Ligand Designing using  Substructure Searching to Explore New Chemical Entities                       ...
AIM OF THIS PROTOCOL:      Scientists always rely on active-site directed ligand designing to design a novel molecule. It ...
really disappearing in the library screening. Hence, we propose the above procedure without creating analogs and there is ...
Go to Pubchem and copy the imatinib’s smiles (only Canonical smiles not Isomeric smiles) or you can copy its InChi KeyGo t...
In this example, we retrieved two molecules having same scaffold and identical chemical structure. But notice that the two...
Go to PharmaGist, upload the ZIP file using Browse option, provide your email ID without spelling mistakes, no of outputph...
Copyrighted material © S.Prasanth Kumar, 2011   7
Clicking on link in the received email will be directed to a page where you can find the results.Copyrighted material © S....
Copyrighted material © S.Prasanth Kumar, 2011   9
INTERPRETATION OF RESULTS OBTAINED:In the eighth page, we can get an overview of all the existing pharmacophore features a...
In the tenth page, we can see the pharmacophore overlaid on aligned 3D ligand molecules (Java Plugin required to visualize...
Copyright © 2011 S.Prasanth Kumar. This is an open access document distributed under the public domain, which permits unre...
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Pharmacophore based ligand-designing_using_substructure_searching_to_explore_new_chemical_entities_(nc_es)

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Pharmacophore based ligand-designing_using_substructure_searching_to_explore_new_chemical_entities_(nc_es)

  1. 1. Pharmacophore-based Ligand Designing using Substructure Searching to Explore New Chemical Entities (NCEs) S.Prasanth Kumar, Bioinformatician CopyrightsCopyright © 2011 S.Prasanth Kumar. This is an open access document distributed under the publicdomain, which permits unrestricted use, distribution, and reproduction in any medium. Thisprotocol should be a demonstration to better understand the concepts and the learners are advised todo it themselves. Don’t forget to acknowledge the contributors.Copyrighted material © S.Prasanth Kumar, 2011 1
  2. 2. AIM OF THIS PROTOCOL: Scientists always rely on active-site directed ligand designing to design a novel molecule. It can be based on fragment baseddrug designing (FBDD) or de novo drug design. This work can be performed if we know the crystallography data (3D structure) ofthe receptor protein. If the 3D structure is not available and having in hands, proven activity against a known protein, structuredetermination of the ligand molecule is done so that the ligand molecular structure can be enhanced to be an efficient binder. Thiscase is known as ligand based drug designing (LBDD). To study the biological activity for a specific receptor protein, lots of ligands having biological activity measured in terms ofIC50 or Ki or MIC50 value and its 3D structure for its identification of pharmacophoric key features, is taken into consideration. Onlyat active-site directed ligand designing, new chemical entities (NCEs) are discovered. In this present protocol, the aim is to identifythe pharmacophore of a known activity molecule (in other words, a patented and an already marketing drug molecule). We shall callit as a pivot/key molecule and a substructure searching on this pivot molecule using its SMILES and/or InChi key chemical formats,will enlist a lots of compounds having similar scaffold. By selecting a wide range of compounds, we can come across a commonpharmacophore key features which are responsible for its biological activity. Here, we stress after overlaying all thepharmacophore features, select some functional groups which has similar pharmacophore feature (e.g. OH group act as hydrogenbond acceptor/donor and it can be placed with NH2 group which has hydrogen bond acceptor and/or donor). In this way, there is apotential way of identifying NCEs having known pharmacophore features and a docking analysis will help us to identify whether isa efficient binder or not. This task greatly reduces the virtual and/or organic combinatorial library screening procedure which hasbeen done on known ligands having broader biological activity spectrum. Now, the specificity and the NCEs identifications areCopyrighted material © S.Prasanth Kumar, 2011 2
  3. 3. really disappearing in the library screening. Hence, we propose the above procedure without creating analogs and there is a highpossibility of developing derivatives which can be patented by you!!!Confusing!!! Contact me at prasanthbioinformatics@gmail.comPROGRAMS/SERVERS USED: 1. NCBI’s PubChem (http://pubchem.ncbi.nlm.nih.gov/) 2. PharmaGist (http://bioinfo3d.cs.tau.ac.il/pharma) 3. Marvin Sketch (Free for Academic usage, www.chemaxon.com)PROTOCOL:Select a molecule which you want to start a work on generating NCEs or derivatives. Structure of Imatinib (marketed by Novartis as GleevecTM)Copyrighted material © S.Prasanth Kumar, 2011 3
  4. 4. Go to Pubchem and copy the imatinib’s smiles (only Canonical smiles not Isomeric smiles) or you can copy its InChi KeyGo to Pubchem Structure Search, select “Identity/Similarity”, paste your smiles or InChi key and hit the Search button leaving allthe parameters default.From the search list, select molecules and download their respective structures in 3D-SDF format. In case, if the 3D-SDF format isnot available, download the 2D-SDF file, open it in Marvin Sketch, Structure > Add > Add Explicit Hydrogens and then chooseCleaning in 3D under the same submenu and save the file in the same format.Copyrighted material © S.Prasanth Kumar, 2011 4
  5. 5. In this example, we retrieved two molecules having same scaffold and identical chemical structure. But notice that the twostructures are having different conformation CID: 10435761 CID: 25235726These structures are of 3D-SDF format. We need structures only on .mol2 format which is the only one format accepted byPharmaGistJust open the structure in any Marvin applications, say Marvin Space and do the following: File>Save As>Type the molecule nameand select Tripos molecule (.mol2 format) to save in prescribed format.We are now uploading three molecules to PharmaGist, the Imatinib, CID 10435761 and CID: 25235726. Create a ZIP file(Desktop>Right Click > New > ZIP folder and name the folder according to your convenience, say imatinibspharma.zip). Now, openthe ZIP folder and paste the three molecular structures in .mol2 format.Copyrighted material © S.Prasanth Kumar, 2011 5
  6. 6. Go to PharmaGist, upload the ZIP file using Browse option, provide your email ID without spelling mistakes, no of outputpharmacophores is 5 (default). Without using advanced options, click on Submit Query button.You will be directed to a page (snapshot in next page) where you can find your submission status. The server will validate ourmolecules, run the program and the result will be emailed to us. Please note that the results will not be displayed after theexecution of the program, they will notify us the results on email providing the link to retrieve the results.Copyrighted material © S.Prasanth Kumar, 2011 6
  7. 7. Copyrighted material © S.Prasanth Kumar, 2011 7
  8. 8. Clicking on link in the received email will be directed to a page where you can find the results.Copyrighted material © S.Prasanth Kumar, 2011 8
  9. 9. Copyrighted material © S.Prasanth Kumar, 2011 9
  10. 10. INTERPRETATION OF RESULTS OBTAINED:In the eighth page, we can get an overview of all the existing pharmacophore features available in all ligand molecules.Under Sort by Score (eighth page, second image), you can see the multiple structural alignment. Here, you can see each and everymolecule was given a chance to act as pivot molecule, upon which the rest two molecules will be aligned. This approach has beenadopted to have a blind search and possibly, get the correct alignment based on repeated iterations on selecting pivot moleculeand aligning the rest of the molecules. We can judge the best alignment using the score 40.530 using CID: 10435761 acted as thepivot molecule. Click on the corresponding row having the header “Jmol” (e.g. J3_1.html and the link will be directed to openanother page: see snapshot of ninth page bottom snapshot).(We can also check the pairwise structure alignment as we do in multiple sequence alignment by clicking on “View Best PairwiseAlignment” header and as usual, you will be directed to another page, which looks like in the top image given at the ninth page).Copyrighted material © S.Prasanth Kumar, 2011 10
  11. 11. In the tenth page, we can see the pharmacophore overlaid on aligned 3D ligand molecules (Java Plugin required to visualize).* Symbol indicates the pivot molecule as we know already. Checking on all the options under the header “Show Molecule” and“Show Features” will help you to study the pharmacophore as reported in page no.10.Uncheck all the options under Show Molecule header, to get an overview what are the pharmacophore features actually aligned.You can see the color scheme adopted for every pharmacophore feature will help you to recognize.Finally, clicking on “Download Pharmacophore and Alignment File” will open up a pop-up window to download/save the file. Pleasenote that this aligned file will be in .mol2 format. Opening this file will get you a structural alignment (superimposed structures).Copyrighted material © S.Prasanth Kumar, 2011 11
  12. 12. Copyright © 2011 S.Prasanth Kumar. This is an open access document distributed under the public domain, which permits unrestricted use,distribution, and reproduction in any medium. If any errors or corrections or comments to make, please feel free to email me atprasanthbioinformatics@gmail.comCopyrighted material © S.Prasanth Kumar, 2011 12

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