The document explores the complexities of drug development and personalized medicine, emphasizing the importance of pharmacogenetics and the role of genetic variation in drug responses. It discusses the lengthy and costly drug development cycle, challenges in drug testing, and the significance of targeted therapies that cater to individual patient profiles. Personalized medicine aims to optimize treatment effectiveness and minimize adverse effects by tailoring medication to specific genetic and metabolic characteristics.

1. Towards Personalized Medicine Michel Dumontier, Ph.D. Assistant Professor of Bioinformatics Department of Biology, Institute of Biochemistry, School of Computer Science Carleton University Ottawa Institute for Systems Biology Ottawa-Carleton Institute for Biomedical Engineering

2. Drug Development Life Cycle Years 0 2 4 6 8 10 12 14 16 Discovery Preclinical Testing (Lab and Animal Testing) Phase I (20-30 Healthy Volunteers used to check for safety and dosage) Phase II (100-300 Patient Volunteers used to check for efficacy and side effects) Phase III (1000-5000 Patient Volunteers used to monitor reactions to long-term drug use) FDA Review & Approval Post-Marketing Testing

3. Drug Discovery aims to identify a lead compound Discovery: Identify the molecular target Design an assay for regulation of activity Identify hits with chemical screening Determine mechanism of action Identify a lead compound with strong binding affinity, K D < 1 μ M Demonstrate therapeutic value with in vivo proof of concept in animals/cell cultures

4. The development phase evaluates drug effectiveness Drugs must overcome numerous challenges chemically stable in stomach (pH 1) not digested by gastrointestinal enzymes absorbed into the bloodstream pass through series of cell membranes not bind tightly to other substances survive xenobiotic detoxification by liver enzymes avoid excretion by kidneys brain: cross blood-brain barrier (blocks polar substances) intracellular receptor: pass through cell membrane

5. Adverse Drug Reactions ADR is one of the leading causes of hospitalization and death 6.7% of hospitalized patients have serious ADRs 0.3% of hospitalized patients have fatal ADRs Known side effects Unavoidable Avoidable Medication errors Product quality defects Preventable adverse events Injury or death Remaining uncertainties Unexpected side effects Unstudied uses Unstudied populations

6. LIPITOR: Known Side Effects Lipitor blocks the production of cholesterol in the body. May reduce risk of hardening of the arteries, which can lead to heart attacks, stroke, and peripheral vascular disease

7. VIOXX: Unknown Side Effects Treatment for Acute Pain increased risk of heart attack and stroke (after 18 months)

8. FDA: Center for Drug Evaluation and Research 2003 - Report to the Nation

9. Cost of developing drugs Global Alliance for Tuberculosis Drug Development www.tballiance.org &quot;The Economics of TB Drug Development&quot; Costs to discover and develop a new anti-TB drug range from $115 million to $240 million. $40 million to $125 million for discovery $76 million to $115 million for preclinical development through Phase III trials

10. Drug Development & Costs Discovery Pre-Clinical Phase I Phase II Phase III FDA COST # Drugs %Total $100M 2000 100% $0.5M 100 5% $0.5M 20 1% $5M 3 0.15% $50M 2 0.10% 1 0.05% ~$156M

11. R&D Spending and New Medicines 38 new medicines in 2004 Cancer Infectious diseases Parkinson’s therapy Radiation contamination Pain alleviation from made from a synthetic form of a sea-snail venom. PhRMA Annual Report 2005-2006

12. An Analysis National Institute for Health Care Management Changing Patterns of Pharmaceutical Innovation, May 2002 Quality of pharmaceutical innovation varies widely. Breakthrough treatments for life threatening diseases TO Minor modifications of drugs that have been on the market for some time.

13. Most drugs approved are only slightly modified

14. Less innovative than you think

15. The Hatch-Waxman Act (1984) Drug Price Competition and Patent Term Restoration Act Open the market to generics immediately after patent expiry, but new tactics to protect Easier for generics to obtain FDA marketing approval Drug Company 30-month stay against generic manufactures that challenge their patents. Additional period (< 5 yrs) of marketing exclusivity in addition to 20 year patent exclusivity Easy patents for drug variants keep generics off the market by protecting their drugs with extra patents of poor quality, filing lawsuits to protect the patents even when the lawsuit will be lost, but getting the extra market exclusivity anyway.

16. Profits as a Percentage of Assets, 2002 Top 7 of Fortune 500 Industries Source: Fortune Magazine, April 14, 2003

17. Drug development has been and still is costly, risky, and lengthy R&D costs have increased , but the industry remains one of the most profitable Pharmaceutical innovation is targeted towards protecting interests The payoffs for improvements in the process are significant The Drug Business

19. Agouron Pharmaceuticals Designed a non-peptidic hydroxamate inhibitor Used structure of recombinant human MMPs bound to various inhibitors Determined key residues, ligand substituents needed for binding Gelatinase A

20. MMPI in Cancer Therapy Design of inhibitors Matrix Metallo Proteinase Inhibitors (MMPI) are a class of cancer therapeutics MMP levels are increased in areas surrounding tumor Degrade extracellular matrix proteins and can lead to spread of cancer Inhibitors can prevent metastasis may also play role in blocking tumor growth Melissa Passino. Structural Bioinformatics in Drug Discovery.

21. “ metallo” in MMP = zinc -> catalytic domain contains 2 zinc atoms MMP catalysis Whittaker et al. Chem. Rev. 1999 , 99 , 2735-2776

22. Peptidic hydroxamate inhibitors Specificity for MMPs over other MPs Better binding But poor oral bioavailability

23. Finding drug leads If we have a target , how do we find some compounds that might bind to it? Classic: exhaustive screening Modern: computational screening!

24. Combinatorial Chemistry Parallel synthetic approach Build on previous products Generate diversity by adding R groups Recover most active compounds Solid phase synthesis Wash away excess reagants & other products Can recover the main product Parallel testing

25. combinatorial synthesis of non-peptide drugs + 1) 2) RXN 1 RXN 2

26. Structure-Based Docking Methods Need 3D structure Scan a virtual library of small molecules and “dock” them to a site of interest on a protein structure Predict binding energy Filters thousands of compounds relatively quickly Top hits can be used for more rigorous computational/experimental characterization and optimization

27. Importance of Structural Bioinformatics Provides a framework for understanding general macromolecular features Automatic identification of binding pockets. Measurement size of surface binding pockets. Speeds up key steps in drug discovery Understand molecular basis for disease Determine potential interactors Identify potential targets which bind small molecules.

28. Structural bioinformatics to design nonpeptidic hydroxylates oral bioavailabity binding anti-growth anti-metastasis repeat…

29. Prinomastat Good oral bioavailability Selective for specific MMPs Evidence showing prevention of lung cancer metastasis in rat and mice models Clinical trials cell lung cancer prostate cancer

30. “If it were not for the great variability among individuals , medicine might as well be a science and not an art ” Sir William Osler, 1892

32. Major sources of variation Single Nucleotide Polymorphisms (SNPs) Single base change in DNA AAGC C TA AAGC T TA Average frequency 1/1000bp SNPs arise as a consequence of mistakes during normal DNA replication Genomic rearrangements Duplications, insertions, deletions

33. Genetics as the basis for variability in drug response Pharmacogenetics The effect of genetic variation on drug response. Pharmacogenomics The application of genomics to the study of human variability in drug response. Pharmacogenetics and pharmacogenomics are expected to play an important role in the development of better medicines for populations and targeted therapies with improved benefit/risk ratios for individuals

34. Personalized Medicine The ability to offer The Right Drug To The Right Patient For The Right Disease At The Right Time With The Right Dosage Genetic and metabolic data will allow drugs to be tailored to patient subgroups

35. Benefits of Personalized Medicine Better matching patients to drugs instead of “trial and error Customized pharmaceuticals may eliminate life-threatening adverse reactions Reduce costs of clinical trials by Quickly identifying total failures Favourable responses for particular backgrounds Improved efficacy of drugs

36. Personalized Medicine : BiDil Combination pill containing two medications for heart failure, cardiovascular disease, and/or diabetes. Clinical trials did not show overall benefit across entire population. Subgroup of African-descent patients showed benefit BiDil approved for use in African-descent patients.

37. Pharmacokinetics and pharmacodynamics are essential to assess the drug efficacy. Pharmacokinetics What the body does to the drug dose, dosage regimen, delivery form Drug fate: Absorption, distribution, metabolism, and elimination of drugs (ADME) Pharmacodynamics What the drug does to the body Biochemical and physiological effects of drugs mechanism of drug action relationship between drug concentration and effect

41. Codeine Metabolism 5-10% codeine is metabolized into morphine by CYP2D6 7% of caucasians have a nonfunctional CYP2D6 variant <2% are CYP2D6 ultrarapid metabolizers which may suffer from opioid intoxication 80% codeine normally converted to glucuronide, eliminated by kidney. inhibition of CYP3A4 or rapid metabolic variants of CYP2D6 during renal failure would show toxicity Gasche Y et al. Codeine intoxication associated with ultrarapid CYP2D6 metabolism. NEJM 2004

42. Drug-Metabolizing Enzymes Pharmacogenomics: Translating Functional Genomics into Rational Therapeutics. Evans and Relling Science 1999 Most DME have clinically relevant polymorphisms Those with changes in drug effects are separated from pie. Phase I: modification of functional groups Phase II: conjugation with endogenous substitutents

43. Cytochrome P450 Enzymes Expressed mainly in liver Act on: Endogenous substrates Xenobiotics including plant and fungal products, pollution, chemicals Drugs (metabolize 50-60%) Typical reaction: Oxidation RH + O 2 + NADPH + H +  ROH + H 2 O + NADP + Sequence diversity: 18 families 43 subfamilies ~60 genes ~100 allelic variants (isoforms)

44. Participation of the CYP Enzymes in Metabolism of Some Clinically Important Drugs S. Rendic Drug Metab Rev 34: 83-448, 2002 CYP Enzyme Examples of substrates 1A1 Caffeine , Testosterone , R-Warfarin 1A2 Acetaminophen , Caffeine , Phenacetin, R-Warfarin 2A6 17  -Estradiol, Testosterone 2B6 Cyclophosphamide, Erythromycin, Testosterone 2C-family Acetaminophen , Tolbutamide (2C9); Hexobarbital, S- Warfarin (2C9,19); Phenytoin, Testosterone , R- Warfarin , Zidovudine (2C8,9,19); 2E1 Acetaminophen , Caffeine , Chlorzoxazone, Halothane 2D6 Acetaminophen , Codeine, Debrisoquine 3A4 Acetaminophen , Caffeine , Carbamazepine, Codeine, Cortisol, Erythromycin, Cyclophosphamide, S- and R-Warfarin , Phenytoin, Testosterone , Halothane, Zidovudine

45. Factors Influencing Activity and Level of CYP Enzymes S. Rendic Drug Metab Rev 34: 83-448, 2002 Red indicates enzymes important in drug metabolism

51. Pharmacogenetics: number of genes affects drug potency Weinshilboum, R. N Engl J Med 2003;348:529-537 Nortryptyline: Anti-depressant

52. Weinshilboum, R. N Engl J Med 2003;348:529-537 Use of probe drugs to determine metabolic activity due to CYP2D6 variants Antihypertensive debrisoquin decreases blood pressure

54. Diagnostics AmpliChip CYP450: Range of drug metabolism phenotypes is observed for individuals based upon the cytochrome P-450 genes

55. Is pharmacogenetics in routine use? NO Science still early. Limited data in public domain. Fragmentation of drug markets is not attractive to drug companies. Many variations not clinically significant Expensive to test for genotype Significantly more challenging to track drug drug interactions

56. CYP3A4 Abundant in liver and intestines and accounts for nearly 50% of CYP450 enzymes. Activity can vary markedly among members of a population Constitutive variability is ~5-fold but can increase to 400-fold through induction and inhibition Activity affected by other drugs: St Johns wort is an inducer, grapefruit juice is an inhibitor Felodipine is a calcium channel blocker (calcium antagonist), a drug used to control hypertension (high blood pressure) 5mg tablet with juice

57. Wilson. PXR, CAR, and drug metabolism. Nat Rev Drug Disc 2002 CYP3A4 mediated Drug-Drug Interaction PXR: pregnane X receptor; RXR: retinoid X receptor Protect against xenobiotics Diverse drugs activate through heterodimer complex Cause drug-drug interactions

60. Quantitative Structure-Activity Relationship (QSAR) find consistent relationship between biological activity and molecular properties, so that these “rules” can be used to evaluate the activity of new compounds. extract features (hydrophobicity, pK, van der Waals radii, hydrogen bonding energy, conformation) build mathematical relationship f(activity|features) automatically assesses the contribution of each feature can be used to make predictions on a new molecule

61. 3D QSAR for CYP3A4

62. 3D QSAR for CYP3A4 with known substrates

63. Drug Metabolic Fate What are the potential by-products of a drug? Going beyond QSAR to de novo predictions Quantify differences in binding due to natural variation.

64. nsSNPs in Ligand Sites of Proteins involved in Disease Of 9.7M SNPs, 778 nsSNPs were located in the predicted binding sites of 484 proteins 611 nsSNPs in 351 disease causing genes (OMIM) over 200 genes not associated with disease Molecular Mechanism? SNP DNA Gene Protein Ligand Binding Disease Daniel Oropeza , 2006 Honours Thesis

65. GTP binding site of S. cerevisiae Homolog 2. The ASP 137 ASN mutation has been shown to cause a decrease in the affinity for GDP (Jones, B et al . 2003). This mutation has been associated with Chylomicron retention disease.

66. Qualitative Functional Inference

67. Genomic Medicine: Predictive, personalized, and pre-emptive

68. Things to Consider Does my doctor know enough about genomic medicine to be advising me? Are there genetic counselors available? Will the test only be for this condition? What if I am susceptible to another disease ? Who will know about this? Doctors… insurance companies ? How exactly will the results be kept secure and in confidence?

70. How much will this cost? More drugs may succeed in clinical trials due to positive outcome for smaller subset Will pharma attempt to recoup costs with a pricier drug? Will public health cover the costs of genetic testing? Reduce overall health cost due to fewer ADRs Should we determine clinically validated genes or should we sequence the genome? How will my insurance premiums be affected?

72. Michel Dumontier [email_address] http://dumontierlab.com