1. Design of Small Molecule Drugs Targeted to RNA RNA Ontology Group May 29 2007

2. Small Molecule and Large Molecule Drug Design “Small Molecule” Drugs –Low MW –Moderately hydrophobic/hydrophilic –Moderately chemical complexity “Biologicals” –Peptides/peptidomimetics –Engineered enzymes –Antisense/RNAi –Need help to enter cells!

3. “New Tools” for Drug Discovery (1980s and 90s) Combinatorial Chemistry Increased the number of available compounds High Throughput Screening (“HTS”) Increases throughput for testing (robotics, databasing) “It’s a Numbers Game”

4. Rational Drug Design = the Opposite of “It’s a Numbers Game” Protein Structure Design small molecule to “fit” and block active site Voila! Doesn’t work! In Silico High Throughput Docking: A rational numbers game

5. Membrane Permeability & “Drug- Likeness” The Lipinski “Rule of Five”

6. Fragment Library Design Fragments must be “lead-like” not “drug- like” MW < 250, allows compound to “grow” Weak binding affinity (will add affinity with growth) Contain polar groups –Insures solubility –Polar groups are reactive –Pick up hydrogen bonding interactions N fragments can cover the chemical space of N 2 compounds

7. Lipinski Rule of 5 Molecular Weight < 500 Daltons cLogP < 5 < 10 Acceptor Groups (O+N) < 5 Donor Groups ( O-H, N-H) Exceptions work by active transport Paromomycin MW 616 Erythromycin MW 734 Tetracycline MW 444 Thiostrepton MW 1665

8. Examples of Small Molecule Molders/Regulators of RNA Secondary Structure in Bacteria 2,6 diaminopurine K d =10 nM Purine K d =100 µM SAH No effect SAM K d =20-200 nM

9. Examples of Small Molecule Molders/Regulators of RNA Secondary Structure in Bacteria L-Lysine K d =1 µM D-Lysine No effect FMN Kd=5 nM Riboflavin Kd=3 µM

10. druggable RNA- binding Protein- binding a b c Lipinski

11. Current Databases Pdb title search: RNA gets 2173 hits: “ternary” Structure description search for ribonucleic acid: 6 hits (2 DNA) NDB search for RNA + ligand: 841 hits, including protein/RNA complex Most ligand databases oriented to search for proteins/ligands

12. Database of RNA Binding Compounds Antibiotics Antibiotics Riboswitch ligands Riboswitch ligands Drug discovery programs (published) Drug discovery programs (published) Published findings of natural products Published findings of natural products 105 compounds in all 105 compounds in all

13. Database of RNA Binding Compounds (caveats) Only 25 compounds had pdb coordinates Only 25 compounds had pdb coordinates Reported K d < 50 μM Reported K d < 50 μM Redundancy: does not include near neighbors Redundancy: does not include near neighbors pdb coordinates did not identify non- contacting substructures pdb coordinates did not identify non- contacting substructures

14. Database of RNA Binding Compounds (further needs) DNA binding compounds DNA binding compounds Classification Classification Correlation with RNA motifs/pharmacophores Correlation with RNA motifs/pharmacophores

16. Fragment based approaches >500k compounds screened assays usually require  M hits Template decoration often prevents interaction Need to reduce MW of weak binders prior to modification HTS Paradigm X HTS requires “right” compounds in library SeeDs Paradigm Drug lead-like fragments No steric inhibition of scaffolds ~ mM binding (Structural Exploration of Exploitable Drug Startpoints) X-ray/NMR Chemistry SBDD Grow potent, selective ligands from fragment