Novel Protease Inhibitors for Hepatitis C

Novel Protease Inhibitors for Hepatitis CBrittany HoltKelly Kerr

4/30/09

Project Goals

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

HCV Background

Hepatitis C: Background Information4.1 million Americans are affected150-200 million people worldwide

Genotype 1 is the most common genotype in America, Japan, and Europe10,000-12,000 Americans die annually

Current medications lead to a sustained virological response of only 40-50% among patients with Genotype 1 HCVCurrent medications have many severe side effects

HCV Life Cycle

Viral Diversity Demands Drug Diversity

Potent drugs already on marketDozens currently being evaluated

So why another drug? Multiple HCV strains HCV inhibitors select for mutants

Modeling versus Laboratory Research

Study of actual virions is very difficult.Lack of suitable cell culturesExtremely small sizeTrouble isolating virions from serum

HCV proteins in databases!

Target Selection Criteria

Tool Available: Modeling Software

Therefore we must select…a viral protein essential for virion production that has a known active site for its function.

Target: Adsorption

E1 and E2

• glycoproteins • associate with cell surface molecules• high variability

Target: Endocytosis/Fusion/Uncoating

Clathrin-coated pit: Entry

Acidic endosomes: Fusion

Uncoating: HCV RNA release

Target: Translation

RNA travels to the rough ER

5’NTR binds to

ribosomal subunits &initiator tRNA

creating theTranslational active complex (HCV polyprotein synthesis)

Target: Posttranslational Processing

Target: ReplicationNS4B • attaches to ER and • forms membranous web

NS3 helicase • unwinds RNA

NS5B • replicates RNA

NS5A • ?

Target: Assembly and Release

• Viral components • Cellular factors • Lipid droplets

Precise mechanisms are not well understood

NS3 Protease

NS3 protease is a viral protein

NS3P cleaves several essential proteinsNS4A, NS4B, NS5A, and NS5B

Active site: Catalytic triad

NS3 needs NS4A (another viral protein)

Catalytic Triad Mechanism

Acylationpeptide bond is cleaved ester linkage is formed between polyprotein carbonyl C and NS3 protease

Deacylationester linkage is hydrolized enzyme is regenerated

Acylation

Deacylation

Hydrogen bonding of Boceprevir to NS3/NS4A protease

Manufacturing and Commercialization Solution Procedure

FDA Clinical TrialsInvestigational New Drug Application (IND)

Sponsors must show the FDA results of preclinical (animal) testingSubmit proposal for clinical trialsFDA decides on safety of proposed trials

Phase 120-80 volunteersGoals:

Determine side effectsDetermine how the drug is metabolized and excreted

Phase 2Evidence of safety must be shown20-300 patients with HCVGoals:

Determine if the drug works on HCVCompare the drug with a placebo or another medicationEvaluate safetyStudy side effects

Phase 3Evidence of effectiveness must be shown200-3,000 patients with HCVGoals:

Effectiveness in different populationsDosage amountsEffectiveness with other drugs

Gantt Chart – Implementation of Boceprevir

Drug Development

FDA Approval

Phase 1

Phase 2

Phase 3

Current Point in process

Wait on FDA Approval of Drug

Manufacturing Plant Implementation

Build Plant

Install Equipment

Train Employees

Production Process Approval

0 2 4 6 8 10 12 14

Timeline for Implementation of SCH 503034

Timeline (Years)

Gantt Chart Analysis

There is a competitive edge to producing the first drug that makes it through clinical trials

Gain reputation for safety and effectivenessRetain a significant market shareIncreased sales

Synthesis of Boceprevir

Alternate Pathways for Synthesis of Boceprevir

Choosing Schemes to Model

Schemes 1 and 4 were modeled in Super Pro

Comparisons between 1, 2, & 3 were not made

Detailed instructions were given for the Scheme 1Can include every operation for Scheme 1Estimated 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

Production Goals

Tablets with 250 mg of active ingredient (SCH503034)

Roughly 7.5 million pills per yearEnough for 1% of HCV infected Americans to take once a day for 24 weeks

Minimal batch timeReduce time equipment spends idleReduce losses that would occur if serious error

Superpro Designer Modeling

Super Pro - Flow Chart

Super Pro - Flow Chart

Gantt Chart – Processing Schedule (Synthesis of Boceprevir)

Gantt Chart – Processing Schedule

One batch requires 149 hrs and over 200 operationsEffective batch time = 57.8 hrs

Use AOT scheduleBottleneck is in Reactor 1Options for optimization

Make process continuousAdd a second R1

h8 16 24 32 40 48 56 64 72 80 88 96 104 112 120 128 136 144 152 160 168 176 184 192 200 208 216 224 232 240 248

day1 2 3 4 5 6 7 8 9 10

Cost EstimatesLow Estimate High Estimate Average Most Likely 95% Confidence

Total Cost Preclinical $ 335,000,000 $ 335,000,000 $ 335,000,000 $ 335,000,000 $ 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

Histogram –Preclinical to Manufacturing Implementation and FCI

Should development continue?

Money spent up to this point$509,642,508

Research and DevelopmentPreclinical (Animal) TrialsClinical Trials

Phase 1Phase 2Part of Phase 3

Comparison with current medication costs

Drug DosageDosage for

Average Man Cost per dosageQuantity Needed Taken Cost per day Cost per week Cost per month

Current Treatments

Ribavirin 11 mg/kg 946 mg $10 per 200 mg capsule 5 Daily $50 $350 $1,525

PEG-IFN α 180 µg 180 µg $600 per 120 µg kit 1 Weekly $600 $2,700

PEG-IFN α 1.5 µg/kg 129 µg $600 per 120 µg kit 1.075 Weekly $645 $2,903

Total Cost $950 $4,225

SCH 503034/Boceprevir

Break even in 10 years $ 20.23 per 200 mg capsule 1 Daily $ 20.23 $ 141.64 $ 617.17

Break even in 9 years $ 21.02 per 200 mg capsule 1 Daily $ 21.02 $ 147.13 $ 641.07

Break even in 8 years $ 22.00 per 200 mg capsule 1 Daily $ 22.00 $ 153.99 $ 670.95

Break even in 7 years $ 23.26 per 200 mg capsule 1 Daily $ 23.26 $ 162.80 $ 709.36

Break even in 6 years $ 24.94 per 200 mg capsule 1 Daily $ 24.94 $ 174.56 $ 760.58

Break even in 5 years $ 27.29 per 200 mg capsule 1 Daily $ 27.29 $ 191.02 $ 832.28

Break even in 4 years $ 30.81 per 200 mg capsule 1 Daily $ 30.81 $ 215.70 $ 939.84

Break even in 3 years $ 36.69 per 200 mg capsule 1 Daily $ 36.69 $ 256.84 $ 1,119.11

Break even in 2 years $ 48.45 per 200 mg capsule 1 Daily $ 48.45 $ 339.13 $ 1,477.63

Break even in 1 year $ 83.71 per 200 mg capsule 1 Daily $ 83.71 $ 585.98 $ 2,553.22

Results

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: $4,2251 month of boceprevir: $2553 with 1 year payback

Predict new molecule that will work better than Boceprevir

Selecting Molecules

Selection CriteriaCompare to Boceprevir

Ki

Inhibition constant: [L] at which ½ of the sites are occupiedSelectivity against human neutrophil elastase (HNE)

Ki (HNE)/ Ki (HCV)Pharmacokinetics

Bioavailability: Fraction that reaches systemic circulation (4-11%)

AUC: Area under the concentration time curve (0.12 uMh )

Solution Procedure

Proposed Molecules

NS3/NS4A Complex

Binding of Drug to Protease

Docking Server Ligands

Docking Server ResultsLigand

Inhibition Constant Ki

(mM)

Catalytic Triad Amino Acids

boundBoceprevir 0.56 3

#1 10.83 2#2 50.92 2#3 0.85 2#4 155.17 2#5 0.24 2#6 48.63 2#7 0.24 2#8 0.09 2#9 0.04 2

#10 0.32 2#11 2.19 3#12 3.14 2#13 1.34 2#14 1.26 3#15 0.33 3#16 5.05 2

Results16 potential drugs have been developedAll bind to catalytic triad

Potential drug #9Lower KiHigher HNE/HCV

We recommend that potential drug #9 be further evaluated using different docking software, and then be synthesized and undergo animal trialsWe also recommend that further research continue on potential drugs 5, 7, 8, 10 and 15

Increase selectivityKeep high binding affinity

Questions?

Docking Server

molecular modeling internet service

developed by Virtua Drug Ltd

capable of calculating the site, geometry, and energy of molecules interacting with proteins

Genetic algorithms

Genotype - translation, orientation, and conformation

Phenotype - atomic coordinates of the ligand

Fitness - total interaction energy of the ligand with the protein

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

Lamarckian genetic algorithm

even more efficient

uses desirable phenotypes to produce desirable genotypes

Synthesis of Boceprevir

FCI

Direct CostsEquipment CostsEquipment InstallationInstrumentation and ControlsPipingElectrical SystemsBuildingsInsulationYard ImprovementsService Facilities

Indirect CostsConstruction ExpensesLegal ExpensesContractor’s feeContingency

Questions?