Antisense Oligonucleotides at Biogen Biogens entry into ASOs with a - PDF document

2/24/2017 Antisense Oligonucleotide Purification Platform: How does it measure up? Kris Ruanjaikaen, Hien Nguyen, Ratnesh Joshi, Yannick Fillon, Robert Gronke March 2, 2017 Antisense Oligonucleotides at Biogen • Biogen’s entry into ASO’s with a strategic alliance with Ionis Pharmaceuticals (Carlsbad, CA) • Pipeline: 8+ drug candidates with a neurology focus including SMA, ALS, Parkinson’s, and Alzheimer's diseases • Our lead ASO drug Spinraza : FDA approval granted in December 2016 for Spinal Muscular Atrophy (SMA) Biogen | Confidential and Proprietary 2 1

2/24/2017 Outline  Introduction: Antisense oligonucleotides (ASOs) o What are they? o How are they made? o Current process vs. Biogen’s platform  Structure and key impurities  Purification platform development o Purification Strategies o Evaluation of Biogen’s pipeline against platform o Process development  Conclusions Biogen | Confidential and Proprietary 3 What are ASOs? Intrathecal Delivery • ASO are short, synthetic nucleic acid chain 8-50 units in length • Designed to bind to complementary mRNA • Has a broad range of effects on protein expression • Biogen has a strong interest in diseases of the brain • Most of our ASO’s require intrathecal (IT) delivery (lumbar puncture) into cerebrospinal fluid • Low concentration DP (< 10 g/L) Rigo F, et al. The Journal of Cell Biology . 2012. 199(1):21-25. Biogen | Confidential and Proprietary 4 2

2/24/2017 ASOs : Structure 5’ DMT blocking group • Used for synthesis Bases reaction sequences • Hydrophobic handle • Will be cleaved off from product 3 5 1 2 • Can be modified for stability Phosphorothioate linkage • S provides resistance to nuclease degradation • Negative charge 2’ modifications • Added stability and potency Chain length varies: 16 – 20 unit Biogen | Confidential and Proprietary 5 ASO Manufacturing Overview: Existing Process Automated Solid-Phase Synthesis grow chemically (3’ to 5’) on a resin bead …one unit at a time… U … G C G Image courtesy of Ionis Pharmaceuticals Purification Biogen’s assessment • High yielding process 1) Reverse- Phase • Good purity Chromatography • Downstream = bottleneck 2) Detritylation • Solvent intensive 3) Precipitation • Not fit into our MFG facility 4) Lyophilization A good process with improvement opportunities Biogen | Confidential and Proprietary 6 3

2/24/2017 ASOs : Key Impurities (Process-Related) Modification Impurities • DMT-on DMT group not cleaved • P=O 3 5 1 2 S replaced by O in phosphorothiate bond • Abasic A base is cleaved off Chain-length Impurities • Failure sequences (N-x) • N-1 • N+1 Biogen | Confidential and Proprietary 7 ASO Impurities: LC-MS Analysis LC Chromatogram (Reverse Phase) DMT-on Failure sequences Mass Spectrum Biogen | Confidential and Proprietary 8 4

2/24/2017 Biogen’s Purification Process Existing Process New Process (ASO-A) Key Rationales Synthesis Synthesis (improved rxns) • Aqueous downstream Hydrophobic Interaction RP-HPLC • Leverage Chromatography (B/E) hydrophobicity similar to RP-HPLC Detritylation Rxn • Cleave DMT group Detritylation Rxn after HIC Anion Exchange • Polishing Chromatography (B/E) chromatography • Robust purity Multiple UF/DF • Streamline formulation Precipitations • Ready-to-fill DS • Reduce process time Lyophilized Liquid DS API Biogen | Confidential and Proprietary 9 Development of ASO Purification Platform Process Biogen | Confidential and Proprietary 10 5

2/24/2017 HIC Overview : Development for first ASO HIC as a capture step to replace RP-HPLC • Facility fit: aqueous process, reduce waste issues • Bind/Elute mode: High resolution of product-related impurities Variables explored (yield vs. purity, process fit) • Resin screening • Kosmotropic salt screening  ammonium sulfate • Leave DMT group on or off? o Location of HIC before detritylation • Optimization o Binding capacity o Wash conditions Elution conditions o Biogen | Confidential and Proprietary 11 HIC Chromatography Typical chromatogram: ASO-A -- UV -- Conductivity AS added to load to increase hydrophobicity (binding) EQ EQ Load / chase Load / chase Wash Wash Elution Elution Strip / CIP Strip / CIP 0.022 • Powerful step for removal of HPLC Purity: ASO-A 0.020 0.018 failure sequences ( ≥ N ± 2) and 0.016 0.014 Load 0.012 small organics AU 0.010 0.008 • Step yield ≥ 85% 0.006 0.004 0.002 • Partially remove impurities Elution 0.000 -0.002 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 similar to product: P=O and N-1 Minutes Does HIC fit across our ASO pipeline? U.S. Patent filled: 62/349,970 How can we develop a process efficiently? Biogen | Confidential and Proprietary 12 6

2/24/2017 HIC Chromatography: Platform Feasibility-- Exploratory Mapping ASO solubility in (NH 4 ) 2 SO 4 Linear (NH 4 ) 2 SO 4 gradient ASO-A UV Absorbance or Conductivity ASO-B ASO-C ASO-D ASO-E ASO-F Conductivity Process Volume • A range of solubility: hydrophobicity • All ASOs bind to HIC depends on ASO sequences • Elution at similar AS concentration • Guideline for loading condition  HIC in B/E mode will work for ASOs without major changes Biogen | Confidential and Proprietary 13 HIC Chromatography: Platform Development Approach Key Developments Step Gradient Chrom • Dynamic binding capacity -- UV • Wash conditions – yield vs. impurity removal -- Conductivity • Elution conditions – yield vs. impurity removal HIC Purification: ASO- B yield vs. impurity LC Data Impurity Wash Elution  Rapid development w/ platform approach  Similar HIC process and yield/ purity performance Biogen | Confidential and Proprietary 14 7

2/24/2017 Detritylation Reaction: Platform Evaluation 5’ 3’ Removal of DMT: W Z Y Z X Y Z W W Y Z X Z W X Y Z W Rxn : platform acidic condition � l � � � � ��� • Simple kinetic model for conversion vs time. • Reaction rates are dependent on 5’ nucleotide (G>U>C)  Platform rxn condition works for all ASO w/ reasonable process time Biogen | Confidential and Proprietary 15 AEX Overview: Development for first ASO AEX evaluated as a polishing step • Bind/Elute mode: High resolution of product-related impurities • Removal of impurities very similar to product (P=O, N-1), DMT-on Variables explored (yield vs. purity, process fit) •Resin screening • Yield vs. Impurity resolution • P=O and DMT-on impurities • Buffer types • Optimization o Binding capacity, Wash and Elution conditions Biogen | Confidential and Proprietary 16 8

2/24/2017 AEX Process & Platform Evaluation • Removal of P=O and N-1 in wash • The ASOs had similar elution salt • Removal of DMT-on in strip • Biogen AEX process will work for the • ≥ 90% yield ASO pipeline Biogen | Confidential and Proprietary 17 AEX Chromatography: Platform Development Approach Key Developments • Binding capacity • Wash conditions – yield vs. impurity removal  Step Gradient Approach • Elution conditions – yield vs. impurity removal AEX Purification: ASO- B  Impurities N+1, N-1, P=O can be partially removed.  Similar process and performance for 2 ASOs Biogen | Confidential and Proprietary 18 9

2/24/2017 UF/DF Overview UF/DF as final formulation • Replacing lengthy precipitation and lyophilization (6 hr vs. several days) • Removal of residual small impurities Membrane Screening 40 PSI 10 PSI 20 PSI 40 PSI Membrane 1, PES S o = C filtrate / C feed Membrane 2, RC Biogen | Confidential and Proprietary 19 UF/DF: Platform Evaluation Process Yield Estimation Design equations Loss during concentration o Loss � 1 � ��� �� � Loss during diafiltration o Loss � 1 � exp��DV ∗ � � � MWCO = 3 kDa ASO-A ASO-B ASO-E 0.006 0.004 0.007 S o Filtrate Feed  3 kDa UF/DF deliver ≥ 90% yield Biogen | Confidential and Proprietary 20 10

2/24/2017 UF/DF Concentration Diafiltration • Good model agreement • High overall yield, 95% • Product concentration, pH, osmolality met target Biogen | Confidential and Proprietary 21 Overall Process Performance: Pilot Data  Overall downstream: high purity and acceptable yield (60-70%)  Consistent platform performance across molecules Biogen | Confidential and Proprietary 22 11