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Drug Docking

Drug Docking. Andrew Harris Mark Clement Kenneth Sundberg. Computer Science Department Brigham Young University. Trypsinogen. Trypsin. Chymotrypsinogen. Chymotrypsin. Enterokinase. Duodenal Cell. Genetic Disease.

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Drug Docking

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  1. Drug Docking Andrew Harris Mark Clement Kenneth Sundberg Computer Science Department Brigham Young University

  2. Trypsinogen Trypsin Chymotrypsinogen Chymotrypsin Enterokinase Duodenal Cell

  3. Genetic Disease • Some diseases caused by over-expression/under-expression of certain proteins or enzymes in a given pathway • Down Syndrome – Trisomy 21, extra 21st chromosome • Larger oral-pharyngeal anatomy • Smaller jaw • Learning disability • Theoretically treatable with drugs

  4. Drug Design Process • Find Targets, Inhibitors, Compounds • Experiment Drug Candidates • Validate in vitro

  5. Information • ZINC, Human Genome Project now make this sequence information available • Reduce time sifting through, predict side effects

  6. PyMOL • A molecular graphics visualization tool • Embedded Python interpreter • Open Source

  7. Drug Docking Algorithm • Searching • Superposition • Rotation • Scoring • Root Mean Square Deviation (RMSD) • Bond Energies

  8. Searching • Centroid Calculation, Geometric Translation • Matrix Multiplication Rotation

  9. Scoring Translation, Rotation Least RMSD score

  10. Drug Docking Algorithm • transpose centroids to the origin • foreach angular displacement in x • foreach angular displacement in y • foreach angular displacement in z • Calculate RMSD • If this RMSD is less than current minimum, save it

  11. Simple 3D Superposition and Alignment

  12. Modified Algorithm

  13. Modified for Drug Docking

  14. Biotin Docking to Streptavidin

  15. Questions?

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