1. Recap: Intermolecular forces and binding Overview of classes of targets for drugs Quantitation of Drug activity (functional assay) EC 50, ED 50, IC 50 Drug binding (binding titration) K D, K I Most common lab techniques (many) Receptors - we covered radioligand binding assay Enzymes - kinetics used (later in quarter)

2. Back to drug discovery: Choose a disease/condition Choose a drug target Inferred from action of drug, poison, natural product, chemical signal found in humans; revealed through genomics Unique to a species or tissue May require multiple targets for effective treatment Choose a bioassay In vivo, in vitro; high throughput screening Two idealized approaches: Start with a known “lead compound” (isolate, purify, identify)…Pharmacophore-based approach Start with a known target structure (isolate, purify, identify)…Target-based approach Hopefully, information about both lead and target are determined.

3. Pharmacophore-based drug design Determine the effects of structural changes on activity of drug: structure-activity relationships (SARs) 1. Data collection: Publications; patents; biological activity; NMR and X-ray data; physiochemical properties 0. Determine identity of a “lead compound”: Screen natural and synthetic banks of compounds for activity Folk medicine Natural ligand Drug already known Computer-aided drug design Computerized search of structural databases

4. Pharmacophore: A specific 3D arrangement of chemical groups common to active molecules and essential to their biological activities Pharmacophore-based drug design This information will result in the identification of a pharmacophore… 2. Analysis: integrate information about drug (and target) to generate hypothesis about activity

5. Why make new lead compounds? Increase activity (make binding stronger) Decrease side effects (increase selectivity) Improve ease and efficiency of administration to patient Potentially find a better synthetic route Pharmacophore-based drug design Approach: Molecular mimicry. If you know the pharmacophore for your target, you can create new lead compounds based on the pharmacophore! 3. Design new structures.

6. Pharmacophore-Based Drug Design Simple example 1: 3D structures are known 1. Data collection: biological activity of lead compound (and other compounds) 2. Analysis: biologically active molecules share the same pharmacophoric features (superimpose 3D structures&find common features)

7. Pharmacophore-Based Drug Design Simple example 1: 3D structures are known 3. Design new structures. New molecular mimic will be tested.

8. Pharmacophore-Based Drug Design Example 2: (A more typical example) Biologically active conformations are not known. 1. Data collection: biological activity. Two molecules below show good activity. Data collection: Determination of biologically active conformation

9. Pharmacophore-Based Drug Design Example 2 (cont): If no 3D data are available, use computers! Bioactive conformations are not always the most stable conformations, but are within about 12kJ/mole or 3kcal/mole) Data collection: Determination of biologically active conformation

10. Pharmacophore-Based Drug Design Generate low energy conformations for each active molecule: A: Etc… B: Etc… 2. Data analysis. Hypothesis: bioactive conformations share 3D features required for activity…Superimpose the generated conformations to define a pharmacophore Example 2 (cont): Data collection: Determination of biologically active conformation

11. Notes: More rigid molecules have fewer conformations – easier to analyze Flexible molecules have many conformations – often must examine conformationally restricted analogs to determine bioactive conformation. (Move from computer to lab: Chemical synthesis of analogs!) (Ex. GABA MC C2.5.2) Superimposing molecules: don’t look at sterics only – think of physical properties of molecule. 3. Design: Use this pharmacophore to design new molecules to test Example 2 (cont): Pharmacophore-Based Drug Design

12. Superimposition of properties: Example Dihydrofolate and methotrexate bind to the catalytic site of dihydrofolate reductase. However, X-ray structures of these complexes shows that they don’t overlap as expected by sterics: Pharmacophore-Based Drug Design

13. Examine electron density distribution of the molecules: Pharmacophore-Based Drug Design Superimposition of properties: Example, cont.

14. Design: use analyzed data to design new compounds - hopefully with better properties Four Methods used to design better drugs: 1.Chemical modification 2.Database searching 3.De novo 4.Manual These approaches generate more data, which yet again can be used to generate new hypotheses and structures, etc. Pharmacophore-Based Drug Design

15. Pharmacophore-based drug design Design method 1: Chemical modification Goal: Determine Structure- activity relationships: What functional groups are important to biological activity?

16. Consequences of chemical modification to drug activity in addition to altering binding interactions: metabolism of drug pharmacokinetics Procedure: Alter or remove groups using chemical synthesis and test the activity of the altered molecule (analog). Infer role of those groups in binding. Pharmacophore-based drug design Design method 1: Chemical modification

17. Initial chemical modification: simplification Example: ergot alkaloids like bromocriptine were starting points for simplified synthetic analogs shown below Once a biologically active compound is found, a common first tactic is to simplify it to determine the essential parts for activity. For complex molecules, this often leads to easier synthesis. Will not be successful if all parts of the molecule are needed for activity Pharmacophore-based drug design Design method 1: Chemical modification

18. Examples: OH isosteres: SH, NH 2, CH 3 O isosteres: S, NH, CH 2 H isostere: F If you change an O to CH 2 - sterics same, but no dipole or lone pair If you change an OH To SH - sterics different, but still a lone pair Pharmacophore-based drug design Design method 1: Chemical modification Common alterations of compounds: replacement of groups with isosteres. Isosteres: atoms or groups of atoms which have the same valency example ?

19. Pharmacophore-based drug design Design method 1: Chemical modification

20. Common alterations of compounds: replacement of groups with bioisosteres. Bioisosteres - different chemical groups with the same biological activity. No restriction on sterics and electronics, unlike classical isosteres. Pharmacophore-based drug design Design method 1: Chemical modification

21. Pharmacophore-based drug design Design method 1: Chemical modification

22. Ring expansion/contractions - changes geometry Ring variations - may add a binding interaction with heteroatom; Pharmacophore-based drug design Design method 1: Chemical modification

23. Extend structure by adding a functional group to lead compound Extend or contract linking chain length between groups Pharmacophore-based drug design Design method 1: Chemical modification

24. Rigidification - limit number of possible conformations Can help identify bioactive conformation Locks molecule in most active conformation - more effective Add a ring Add rigid groups Pharmacophore-based drug design Design method 1: Chemical modification

25. Rigidification (continued) Add a bulky groups (but recall it may not just affect conformaion; it may affect sterics Alter Stereochemistry: usually different stereoisomers have different activity Pharmacophore-based drug design Design method 1: Chemical modification

26. Binding role of hydroxy groups: H-bond donor or acceptor Convert to: methyl ether (no H-bond donor now; maybe steric problem) an ester (no H-bond donor now; poor H-bond acceptor; maybe steric problem) Pharmacophore-based drug design Design method 1: Chemical modification Probing specific functional groups in a molecule

27. methyl ether (no H-bond donor now; still H-bond acceptor; maybe steric problem) an ester (no H-bond donor now; poor H-bond acceptor; maybe steric problem) Binding role of hydroxy groups (continued): Probing specific functional groups in a molecule

28. Binding role of amino groups: H-bond donor (if N-H is present) or acceptor; ionic (protonation of N to form a salt; recall pKa) Convert to: amide (no protonation; no H-bond acceptor now; steric problem?) Tertiary amine (no H-bond donor now; still H-bond acceptor; sterics?) Binding role of aromatic rings, alkenes: hydrophobic; cation-pi Convert to: Saturated compound (not effective overlap; no pi system; more flexible) Probing specific functional groups in a molecule

29. Binding role of ketones: H-bond acceptor; dipole-dipole Convert to: Alcohol (geometry change can weaken H-bond or dipole-dipole) Probing specific functional groups in a molecule

30. Binding role of alkyl substituents: hydrophobics/sterics Convert to: Longer (homologation) or differently-branched groups Alkyl groups most easily modified are Probing specific functional groups in a molecule

31. Binding role of alkyl substituents (continued) Notes: Recall impact of lipophilicity on drug transport through body Changing alkyl groups may also affect the preferred conformation of the molecule! Probing specific functional groups in a molecule

32. Example: Nifedipine analogs Chemical synthesis of analogs help validate or refute hypotheses regarding mechanism of action/mode of binding - part of design Probing specific functional groups in a molecule Binding role of alkyl substituents (continued)

33. Binding role of aryl substituents: various/ sterics Convert to: Same substituents at different locations Different substituents: Recall substituent effects in organic chem! Substituents may affect each others’ properties (pKa) Probing specific functional groups in a molecule

34. Example: beta-adrenergic drugs, chemically related to adrenaline and noradrenaline. Probing specific functional groups in a molecule Binding role of aryl substituents: (continued)

35. Binding role of amides: H-bond acceptor; dipole-dipole Convert to: Hydrolysis products (but will lose a piece); reduce (no more H-bond acceptor Probing specific functional groups in a molecule

36. As computer analysis becomes more widespread, a pharmacophore will be less “visual” and more numerical, with numerical scoring of properties Pharmacophore-based drug design Design method 1: Chemical modification Activity data for modified drugs leads to a better pharmacophore

37. Use databases of known compounds – no new synthesis! Be careful of multiple conformations Content of database is crucial Example. Protein kinase C enzymes are targets for chemotherapeutic intervention against cancer. The pharmacophore was deduced from active phorbol esters like PDBU Pharmacophore-based drug design Design method 2: Database searching a. 3D Search for a 3D pharmacophore

38. The 3D database search led to the discovery of a new potent protein kinase C inhibitor that is chemically very different from the original reference phorbol esters. Alignment of the two: Pharmacophore-based drug design Design method 2: Database searching Start over with this “hit” as a new lead; chemical modification, etc…

39. b. 3D Shape searching on Databases - also finds chemically different compounds, but is successful only if the pharmacophore is also incorporated Pharmacophore-based drug design Design method 2: Database searching

40. Assemble disconnected functional groups (pharmacophoric groups) with spacers with or without computer algorithms; using models or computer modeling software Example. 5-alpha reductase inhibitors inhibit the metabolism of testosterone, and are used to treat prostate hyperplasia. The steroid structure has side effects. Replacement with other structures should help... Pharmacophore-based drug design Design methods 3&4: De novo design and Manual design

41. Computer algorithm was used to obtain the following compounds: Overlay of one “hit”: Other “hits” Pharmacophore-based drug design Design methods 3&4: De novo design and Manual design

42. Patrick, G. L. An Introduction to Medicinal Chemistry; Oxford University Press: New York, NY, 2001 Silverman, R. B. The Organic Chemistry of Drug Design and Drug Action ; Academic Press: San Diego, CA, 1992. Thomas, G. Medicinal Chemistry An Introduction; John Wiley and Sons, Ltd.: New York, NY, 2000. Williams, D. A.; Lemke, T. L. Foye’s Principles of Medicinal Chemistry; Lippincott Williams and Wilkins, New York, NY, 2002. Molecular Conceptor, Synergix: C1 “Rational Drug Design” C2 “Structure Activity Relationships” E1-3 “Pharmacophore-Based Drug Design” References