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SOME EXAMPLES

SOME EXAMPLES. CHRISTOPH PFISTERER DAN MIHAILESCU JENNIFER REED. Does the gp120 recognition peptide have a similar structure in all clades of HIV-1 ?. 11 Sequences in 9 clades A1 LEU PRO CYS ARG ILE LYS GLN PHE ILE ASN MET TRP GLN GLU VAL +2

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SOME EXAMPLES

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  1. SOME EXAMPLES

  2. CHRISTOPH PFISTERER DAN MIHAILESCU JENNIFER REED

  3. Does the gp120 recognition peptide have a similar structure in all clades of HIV-1 ? 11 Sequences in 9 clades • A1 LEU PRO CYS ARG ILE LYS GLN PHE ILE ASN MET TRP GLN GLU VAL +2 • B1 LEU PRO CYS ARG ILE LYS GLN ILE VAL ASN MET TRP GLN GLU VAL +2 • C1 ILE PRO CYS ARG ILE LYS GLN ILE ILE ASN MET TRP GLN GLU VAL +2 • D2 LEU PRO CYS ARG ILE LYS PRO ILE ILE ASN MET TRP GLN GLU VAL +2 • E2 LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN MET TRP GLN GLY VAL +3 • E3 LEU PRO CYS LYS ILE LYS GLN ILE ILE LYS MET TRP GLN GLY VAL +4 • F1 LEU LEU CYS LYS ILE LYS GLN ILE VAL ASN LEU TRP GLN GLY VAL +2 • G2 LEU PRO CYS LYS ILE LYS GLN ILE VAL ARG MET TRP GLN ARG VAL +5 • 1A0 LEU PRO CYS LYS ILE LYS GLN ILE VAL ASN MET TRP GLN ARG VAL +4 • 2A3 LEU GLN CYS ARG ILE LYS GLN ILE VAL ASN MET TRP GLN LYS VAL +4 • OC4 ILE PRO CYS LYS ILE LYS GLN VAL VAL ARG SER TRP ILE ARG GLY +5

  4. Questions Are the gp120 recognition sequence peptides structured in aqueous solution?

  5. Threading of sequences on the peptide backbone LEU PRO CYS ARG ILE LYS GLN PHE ILE ASN MET TRP GLN GLU VAL  ILE PRO CYS LYS ILE LYS GLN VAL VAL ARG SER TRP ILE ARG GLY A1 oc4

  6. Molecular Dynamics Simulation Setup • Box dimensions: 53x40x40 Ǻ • Explicit water molecules (TIP3P) (~8600 atoms) • Explicit ions (Sodium and Chloride, 26 ions in total); physiological salt: 0.23M • ~240 peptide atoms => approx. 8900 atoms in total • Uncharged system • NPT ensemble: 300K, 1atm • 5ns simulation time for each strain => 55ns total simulation time

  7. RMSD (A²) Time (ps) Root Mean Square Coordinate Deviation

  8. MD simulations M D T

  9. Convergence of gp120 peptide structure from three different experimental starting geometries

  10. Questions Are the gp120 recognition sequence peptides structured in aqueous solution? Do the structures of peptides from different clades resemble each other?

  11. Dihedralangles  

  12. Questions Are the gp120 recognition sequence peptides structured in aqueous solution? Do the structures of peptides from different clades resemble each other? Does the consensus structure present a common shape/electrostatic surface?

  13. Shape and electrostatic properties conserved.

  14. Questions Are the gp120 recognition sequence peptides structured in aqueous solution? Do the structures of peptides from different clades resemble each other? Does the consensus structure present a common shape/electrostatic surface? Can the consensus shape/electrostatic surface be mimicked with a synthetic molecule? Can this molecule be used as a lead for vaccine design?

  15. Cancer Biotechnology. Detection of Individual p53-Autoantibodies in Human Sera

  16. Rhodamine 6G

  17. Fluorescence Quenching of Dyes by Trytophan Quencher MR121 Dye

  18. Fluorescently labeled Peptide ?

  19. Analysis r

  20. Strategy: Healthy Person Serum Cancer Patient Serum Quenched Fluorescent Results:

  21. Drug Design Finding the Right Key for the Lock

  22. Ligand Protein Complex Ligand Binding. physicochemical understanding vibrational changes?

  23. STEFAN FISCHER Bovine Pancreatic Trypsin Inhibitor Frequency Shifts Normal Mode Analysis Vibrational Change on Burial of a Water Molecule

  24. Dissecting the Vibrational Entropy Change on Protein/Ligand Binding: Burial of a Water Molecule in BPTI Librational modes = 9.4 cal mol-1 K-1 Softening of protein = 4.0 cal mol-1 K-1

  25. Frequency Shifts Change in Entropy due to Frequency Shifts

  26. complexed uncomplexed Vibrational Thermodynamics Gvib = -4.0  1.0 kcal/mol -TSvib= -6.0  1.5 kcal/mol Hvib = +2.0  0.5 kcal/mol j VIBRATIONAL FREQUENCY DISTRIBUTION ERIKA BALOG TORSTEN BECKER Vibrational Change on Methotrexate Binding to Dihydrofolate Reductase

  27. Drug Design High Throughput Screening 104 ligands per day  But: Hit Rate 10-6 per ligand

  28. FRAUKE MEYER What is the binding free energy? entropic effects protein polar and non-polar interactions with the solvent ligand k1 k-1 polar and non-polar protein-ligand interactions water complex

  29. Electrostatics: Thermodynamic Cycle + +

  30. Methods • flexibility (Jon Essex) • MD (Daan van Aalten) • scoring functions, virtual screening (Martin Stahl, Qi Chen) • prediction of active sites (Gerhard Klebe) • active site homologies

  31. Ligands: set n0

  32. Fast Calculation of Absolute Binding Free Energies: Interaction of Benzamidine Analogs with Trypsin Benzamidine-like Trypsin Inhibitors Energy Terms and Results - van der Waals protein:ligand - hydrophobic effect (surface area dependent) - electrostatic interactions (continuum approach) - translational, rotational, vibrational degrees of freedom End ss 2004

  33. Results: Binding free energies RMSD(flex) = 1.3 kcal/mol RMSD(fix) = 3.2 kcal/mol Fig: Calculated versus experimental binding free energies

  34. CONCLUSION: Including flexibility improves the prediction of binding free energies OUTLOOK: Introduction of polarisation energy Automation of the free energy calculation protocol THANKS! Jeremy, Stefan, Sonja, Bogdan, girls’ room

  35. Results: Energy contributions Fig: Range of calculated binding free energies and the contributing terms for the ligands of set n0 and n1

  36. Successes and failures instructure-based drug design Mercedes L. Dragovits

  37. The drug discovery and development pipeline

  38. Choice of a target • Link to a human disease • Binds a small molecule to carry out a function • The drug competes with the natural molecule

  39. Theiterative processof SBDD

  40. Overview of the process: first cycle • Cloning, purification, structure determination of the target • X-ray-crystallography • NMR • Compounds or fragments of compounds are placed in selected regions of the target using computer algorithms • Test the best compounds with biochemical assays

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