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S.Prasanth Kumar, Bioinformatician Pharmacogenomics & Drug Design de novo  Drug Design S.Prasanth Kumar, Bioinformatician ...
From Scratch DE NOVO  DESIGN The design of bioactive compounds by incremental construction of a ligand model within a mode...
Primary Target Constraints PRIMARY TARGET CONSTRAINTS (The binding affinity of a ligand to the particular biological targe...
Receptor-based scoring Scoring functions rank the generated structures and thereby suggest which structures are the most p...
Ligand-based scoring Particular biological target is  unavailable  but one or more binding molecules are known Pseudo-Rece...
Secondary Target Constraints Constraints other than the binding affinity are secondary constraints. Candidate compounds wi...
Principles of structure-based ligand assembly Link/grow strategy
Principles of structure-based ligand assembly Lattice strategy
Search Space Exploration
Why De novo Drug Design ? Complementary strategy to HTS NCEs that were designed taking into consideration several aspects ...
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De novo drug designing strategies

De novo drug design

  1. 1. S.Prasanth Kumar, Bioinformatician Pharmacogenomics & Drug Design de novo Drug Design S.Prasanth Kumar, Bioinformatician S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA www.facebook.com/Prasanth Sivakumar FOLLOW ME ON ACCESS MY RESOURCES IN SLIDESHARE prasanthperceptron CONTACT ME [email_address]
  2. 2. From Scratch DE NOVO DESIGN The design of bioactive compounds by incremental construction of a ligand model within a model of the receptor or enzyme active site, the structure of which is known from X-ray or NMR data a de novo design program how to assemble the candidate compounds; how to evaluate their potential quality; how to sample the search space effectively.
  3. 3. Primary Target Constraints PRIMARY TARGET CONSTRAINTS (The binding affinity of a ligand to the particular biological target) Receptor-based Derivation of Interaction Site Ligand-based (subdivided into hydrogen bonds, electrostatic and hydrophobic interactions) HSITE – hydrogen acceptor–donor pairs HIPPO - lipophilic
  4. 4. Receptor-based scoring Scoring functions rank the generated structures and thereby suggest which structures are the most promising ones Force fields : Energy Minimization LEGEND Empirical scoring functions are a weighted sum of individual ligand–receptor interaction types commonly supplemented by penalty terms, such as the number of rotatable ligand bonds. LUDI Knowledge-based scoring is grounded on a statistical analysis of ligand–receptor complex structures. The frequencies of each possible pair of atoms in contact to each other are determined. SmoG
  5. 5. Ligand-based scoring Particular biological target is unavailable but one or more binding molecules are known Pseudo-Receptor Pharmacophore
  6. 6. Secondary Target Constraints Constraints other than the binding affinity are secondary constraints. Candidate compounds with an increased chance of oral bioavailability can be obtained by filtering the designed structures with Lipinski’s rule of- five A list of undesirable substructures for ease in the synthesis
  7. 7. Principles of structure-based ligand assembly Link/grow strategy
  8. 8. Principles of structure-based ligand assembly Lattice strategy
  9. 9. Search Space Exploration
  10. 10. Why De novo Drug Design ? Complementary strategy to HTS NCEs that were designed taking into consideration several aspects of lead- and drug-likeness and synthetic accessibility De novo design offers a broader exploration of chemical space and therefore makes it possible to identify novel ligand scaffolds
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De novo drug designing strategies

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