1. Brittany Holt Kelly Kerr 4/30/09

2. Determine manufacturing and commercialization efforts, including the FDA approval process for a new orally available hepatitis C NS3/NS4A protease inhibitor (SCH 503034, Boceprevir) Determine a novel molecule that can prevent the production and release of infectious HCV particles. Predict the effectiveness of the new molecule. Compare this to the effectiveness of drugs that are currently being developed. Modify molecules based on binding affinity tests

4. 4.1 million Americans are affected 150-200 million people worldwide Genotype 1 is the most common genotype in America, Japan, and Europe 10,000-12,000 Americans die annually Current medications lead to a sustained virological response of only 40-50% among patients with Genotype 1 HCV Current medications have many severe side effects

7. Study of actual virions is very difficult. Lack of suitable cell cultures Extremely small size Trouble isolating virions from serum HCV proteins in databases!

8. Tool Available: Modeling Software Therefore we must select… a viral protein essential for virion production that has a known active site for its function.

9. E1 and E2 glycoproteins associate with cell surface molecules high variability

10. Clathrin-coated pit: Entry Acidic endosomes: Fusion Uncoating: HCV RNA release

11. RNA travels to the rough ER 5’NTR binds to ribosomal subunits & initiator tRNA creating the Translational active complex (HCV polyprotein synthesis)

13. NS4B attaches to ER and forms membranous web NS3 helicase unwinds RNA NS5B replicates RNA NS5A ?

14. Viral components Cellular factors Lipid droplets Precise mechanisms are not well understood

15. NS3 protease is a viral protein NS3P cleaves several essential proteins NS4A, NS4B, NS5A, and NS5B Active site: Catalytic triad NS3 needs NS4A (another viral protein)

16. Acylation peptide bond is cleaved ester linkage is formed between polyprotein carbonyl C and NS3 protease Deacylation ester linkage is hydrolized enzyme is regenerated

21. Investigational New Drug Application (IND) Sponsors must show the FDA results of preclinical (animal) testing Submit proposal for clinical trials FDA decides on safety of proposed trials Phase 1 20-80 volunteers Goals: Determine side effects Determine how the drug is metabolized and excreted Phase 2 Evidence of safety must be shown 20-300 patients with HCV Goals: Determine if the drug works on HCV Compare the drug with a placebo or another medication Evaluate safety Study side effects Phase 3 Evidence of effectiveness must be shown 200-3,000 patients with HCV Goals: Effectiveness in different populations Dosage amounts Effectiveness with other drugs

23. There is a competitive edge to producing the first drug that makes it through clinical trials Gain reputation for safety and effectiveness Retain a significant market share Increased sales

26. Schemes 1 and 4 were modeled in Super Pro Comparisons between 1, 2, & 3 were not made Detailed instructions were given for the Scheme 1 Can include every operation for Scheme 1 Estimated batch times and costs for Schemes 2 and 3 would be unfairly low Reagents used in Scheme 1 are more readily obtainable Cost should be more accurate Cost should be lower

27. Tablets with 250 mg of active ingredient (SCH503034) Roughly 7.5 million pills per year Enough for 1% of HCV infected Americans to take once a day for 24 weeks Minimal batch time Reduce time equipment spends idle Reduce losses that would occur if serious error

32. One batch requires 149 hrs and over 200 operations Effective batch time = 57.8 hrs Use AOT schedule Bottleneck is in Reactor 1 Options for optimization Make process continuous Add a second R1

33. Low EstimateHigh EstimateAverageMost Likely95% Confidence Total Cost Preclinical $ 335,000,000 Total Cost Clinical $ 66,366,260 $ 277,294,933 $ 171,830,596 $ 188,845,040 $ 239,703,266 Total Cost Preclinical and Clinical $ 401,366,260 $ 612,294,933 $ 506,830,596 $ 509,642,508 $ 574,801,384 Total Cost Preclinical to Manufacturing Implementation $ 405,379,075 $ 643,897,990 $ 524,638,532 $ 528,080,243 $ 600,385,656 Total Manufacturing Cost per year $ 48,255,217 $ 147,852,741 $ 98,053,979 $ 96,167,982 $ 128,423,759 Fixed Capital Investment $ 4,296,135 $ 36,421,069 $ 20,358,602 $ 14,526,282 $ 30,729,118 Working Capital (6 months) $ 24,127,608 $ 73,926,370 $ 49,026,989 $ 47,239,802 $ 64,252,062 Total Capital Investment $ 52,551,352 $ 184,273,810 $ 118,412,581 $ 128,929,085 $ 159,413,694

35. Money spent up to this point $509,642,508 Research and Development Preclinical (Animal) Trials Clinical Trials Phase 1 Phase 2 Part of Phase 3

36. DrugDosage Dosage for Average ManCost per dosage Quantity NeededTakenCost per dayCost per weekCost per month Current Treatments Ribavirin11 mg/kg946mg$10per 200 mg capsule5Daily$50$350$1,525 PEG-IFN α180 µg180µg$600per 120 µg kit1Weekly$600$2,700 PEG-IFN α1.5 µg/kg129µg$600per 120 µg kit1.075Weekly$645$2,903 Total Cost$950$4,225 SCH 503034/Boceprevir Break even in 10 years $ 20.23per 200 mg capsule1Daily $ 20.23 $ 141.64 $ 617.17 Break even in 9 years $ 21.02per 200 mg capsule1Daily $ 21.02 $ 147.13 $ 641.07 Break even in 8 years $ 22.00per 200 mg capsule1Daily $ 22.00 $ 153.99 $ 670.95 Break even in 7 years $ 23.26per 200 mg capsule1Daily $ 23.26 $ 162.80 $ 709.36 Break even in 6 years $ 24.94per 200 mg capsule1Daily $ 24.94 $ 174.56 $ 760.58 Break even in 5 years $ 27.29per 200 mg capsule1Daily $ 27.29 $ 191.02 $ 832.28 Break even in 4 years $ 30.81per 200 mg capsule1Daily $ 30.81 $ 215.70 $ 939.84 Break even in 3 years $ 36.69per 200 mg capsule1Daily $ 36.69 $ 256.84 $ 1,119.11 Break even in 2 years $ 48.45per 200 mg capsule1Daily $ 48.45 $ 339.13 $ 1,477.63 Break even in 1 year $ 83.71per 200 mg capsule1Daily $ 83.71 $ 585.98 $ 2,553.22

37. Development and Manufacturing will take approximately 14 years The most likely total cost from research and development through plant construction will cost $528 million This is less than the average cost for development of a drug, $802 million, as reported in the Journal of Health Economics This cost is expensive, but relative to other drugs the cost of research and commercialization for boceprevir is reasonable 1 month of current treatments: $4,225 1 month of boceprevir: $2553 with 1 year payback

39. Selection Criteria Compare to Boceprevir K i Inhibition constant: [L] at which ½ of the sites are occupied Selectivity against human neutrophil elastase (HNE) K i (HNE)/ K i (HCV) Pharmacokinetics Bioavailability: Fraction that reaches systemic circulation (4-11%) AUC: Area under the concentration time curve (0.12 uMh )

45. Ligand Inhibition Constant Ki (mM) Catalytic Triad Amino Acids bound Boceprevir0.563 #110.832 #250.922 #30.852 #4155.172 #50.242 #648.632 #70.242 #80.092 #90.042 #100.322 #112.193 #123.142 #131.342 #141.263 #150.333 #165.052

46. 16 potential drugs have been developed All bind to catalytic triad Potential drug #9 Lower Ki Higher HNE/HCV We recommend that potential drug #9 be further evaluated using different docking software, and then be synthesized and undergo animal trials We also recommend that further research continue on potential drugs 5, 7, 8, 10 and 15 Increase selectivity Keep high binding affinity

48. molecular modeling internet service developed by Virtua Drug Ltd capable of calculating the site, geometry, and energy of molecules interacting with proteins

49. Genetic algorithms Genotype - translation, orientation, and conformation Phenotype - atomic coordinates of the ligand Fitness - total interaction energy of the ligand with the protein

50. Genetic algorithms Individuals that have low fitness die New individuals are created by inheriting genes from either of two parents Mutations also occur randomly DockingServer can predict where and how a ligand will bind to be most energetically favorable

51. Lamarckian genetic algorithm even more efficient uses desirable phenotypes to produce desirable genotypes

53. Direct Costs Equipment Costs Equipment Installation Instrumentation and Controls Piping Electrical Systems Buildings Insulation Yard Improvements Service Facilities Indirect Costs Construction Expenses Legal Expenses Contractor’s fee Contingency