OA19808A - Methods for the treatment of subjects having a hepatitis B virus (HBV) infection. - Google Patents

Methods for the treatment of subjects having a hepatitis B virus (HBV) infection. Download PDF

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OA19808A
OA19808A OA1201900408 OA19808A OA 19808 A OA19808 A OA 19808A OA 1201900408 OA1201900408 OA 1201900408 OA 19808 A OA19808 A OA 19808A
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rnai agent
protein
hbv vaccine
based hbv
nucleic acid
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OA1201900408
Inventor
Laura Sepp-Lorenzino
Ulrike Protzer
Thomas MICHLER
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Alnylam Pharmaceuticals, Inc.
Technische Universität München
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Application filed by Alnylam Pharmaceuticals, Inc., Technische Universität München filed Critical Alnylam Pharmaceuticals, Inc.
Publication of OA19808A publication Critical patent/OA19808A/en

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Abstract

The present invention provides methods for the treatment of a subject having a Hepatitis B virus (HBV) infection, e.g., a chronic HBV infection, using a combination of an RNAi agent that targets HBV and an HBV vaccine. It is disclosed a RNAi agent and an HBV vaccine for use in treatment of HBV infection, comprising sequentially administering to the subject having an HBV infection: a) an RNAi agent that inhibits expression of at least three HBV transcripts, wherein the RNAi agent forms a double stranded region; b) a protein-based vaccine comprising a first HBV core antigen (HBcAg) polypeptide, and a first HBV surface antigen (HBsAg) polypeptide; and c) a nucleic acid-based vaccine comprising an expression vector construct encoding a second HBcAg polypeptide, and/or a second HBsAg polypeptide, wherein the second HBcAg polypeptide, and/or the second HBsAg polypeptide, shares at least one epitope with at least one of the first HBcAg polypeptide, and/or the first HBsAg polypeptide.

Description

METHODS FOR THE TREATMENT OF SUBJECTS HAVING A HEPATITIS B VIRUS (HBV) INFECTION
RELATED APPLICATIONS
This application claims the benefit of priority to U.S. Provisional Patent Application No.
62/486,618, filed on April 18,2017, U.S. Provisional Patent Application No. 62/553,358, filed on September 1,2017, U.S. Provisional Patent Application No. 62/646,978, filed on March 23,2018, and U.S. Provisional Patent Application No. 62/655,862, filed on April 11,2018. The entire contents of each of the foregoing provisional patent applications are incorporated herein by reference.
SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on April 12,2018, is named 121301-07220_SL.txt and is 429,841 bytes in size.
BACKGROUND OF THE INVENTION
Hepatitis B virus (HBV) is an enveloped DNA virus that infects the liver that causes ' hepatocellular necrosis, inflammation, and is a major risk factor for development of cirrhosis and hepatocellular carcinoma (HCC). The World Health Organization (WHO) estimâtes that there are 240 20 million chronically HBV infected individuals worldwide largely in low to middle income countries and that about 650,000 people will die annually of complications from HBV infection. Although an effective HBV vaccine is available and efforts to vaccinate infants at birth hâve been effective in reducing incidence and prevalence of HBV infection, such programs do not hâve a demonstrable effect on death rates for years (WHO Guidelines for prévention, care and treatment of persons with chronic Hepatitis B Infection, 2015 at apps.who.int/iris/bitstream/10665/154590/l/9789241549059_eng.pdf?ua=l&ua=l).
A number of therapeutic agents hâve been developed for the treatment of HBV that effectively reduce the disease burden of HBV infection, but they are not typically curative as they do not fully eliminate ail réplicative forms of the virus including the covalently closed circular DNA 30 (cccDNA) that résides in the hépatocyte nucléus and becomes a template for viral réplication and transcription of viral RNAs. Nucléotide and nucleoside analogs, typically considered to be the gold standard for treatment of chronic HBV infection due to their safety and efficacy, are effective in suppressing HBV réplication, but they do not eliminate cccDNA, do not prevent expression of viral proteins, must be dosed chronically, and can resuit in the development of résistance. Further, 35 treatment with nucleot(s)ide inhibitors does not fully mitigate the risk of the development of hepatocellular carcinoma (HCC) which remains significant (about 7% in 5-7 years despite treatment). Interferon-based thérapies can resuit in sefo-conversion and cure of about 10-15% of patients allowing discontinuation of treatment, but the agents hâve severe side effects and must be refrigerated for long term storage making them less désirable for use in countries where HBV infection is most prévalent.
Treatment of chronic HBV is further complicated by the ability of HBV to évadé or suppress the immune response resulting in persistence of the infection. The HBV proteins hâve immune5 inhibitory properties, with hepatitis B s antigen (HBsAg) comprising the overwhelming majority of HBV protein in the circulation of HBV infected subjects. Additionally, while the removal (via séroconversion) of hepatitis B e antigen (HBeAg) or réductions in sérum viremia are not correlated with the development of sustained control of HBV infection off treatment, the removal of sérum HBsAg from the blood (and séroconversion) in HBV infection is a well-recognized prognostic indicator of antiviral response to treatment which will lead to control of HBV infection off treatment. However, this only occurs in a small fraction of patients receiving immunotherapy. Therefore, it is possible, although rare, for patients to mount a sufficiently robust immune response to suppress or clear an HBV infection resulting in at least a functional cure of the disease.
SUMMARY OF THE INVENTION
The invention provides RNAi agents and HBV vaccines for use in treatment of hepatitis B virus (HBV) infection and methods for the treatment of a subject having a hepatitis B virus (HBV) infection, e.g., a chronic HBV infection, which includes a combination therapy or treatment regimen including an RNAi agent targeting at least one HBV transcript and a therapeutic vaccination.
Accordingly, in one aspect, the présent invention provides RNAi agents and HBV vaccines for use in treatment of hepatitis B virus (HBV) infection and methods for treating a subject having a hepatitis B virus (HBV) infection, e.g., a chronic HBV infection. The methods include a regimen which includes administering, e.g., sequentially administering, to the subject having the HBV infection, an RNAi agent that targets at least three HBV transcripts, wherein the RNAi agent comprises a sense strand and an antisense strand; a protein-based vaccine comprising an HBV core antigen (HBeAg) and an HBV surface antigen (HBsAg); and a nucleic acid-based vaccine comprising an expression construct encoding an HBeAg or an HBsAg, wherein the construct encodes a protein that shares an epitope with the protein-based vaccine, thereby treating the subject.
In another aspect, the présent invention provides a regimen for treating a subject having a hepatitis B virus (HBV) infection, e.g., a chronic HBV infection. The regimen includes the use of an RNAi agent that targets at least three HBV transcripts, wherein the RNAi agent comprises a sense strand and an antisense strand; a protein-based vaccine comprising an HBV core antigen (HBeAg) and an HBV surface antigen (HBsAg); and a nucleic acid-based vaccine comprising an expression construct encoding an HBeAg or an HBsAg, wherein the construct encodes a protein that shares an epitope with the protein-based vaccine.
In one embodiment, the HBeAg protein, or immunogenic fragment thereof, shares an epitope with the HBV core antigen (HBeAg) polypeptide, or immunogenic fragment thereof, présent in the protein-based vaccine and/or the HBsAg protein, or immunogenic fragment thereof, shares an epitope with the HBV surface antigen (HBsAg) polypeptide, or immunogenic fragment thereof, présent in the protein-based vaccine.
In certain embodiments, the RNAi agent comprises at least one modified nucléotide.
In cértain embodiments, the nucleic acid-based vaccine comprises an expression construct encoding an HBcAg and an HBsAg.
In certain embodiments, the RNAi agent targeting HBV is administered to the subject at least two times.
In certain embodiments, the RNAi agent targeting HBV administered to the subject decreases HBsAg in the sérum of the subject by at least 0.5 log 10 lU/ml. In certain embodiments, the subject has at least a 0.5 loglO lU/ml decrease in HBsAg in sérum prior to administration of the first dose of the protein based vaccine. In certain embodiments, the subject has at least a 1 loglO lU/ml decrease in HBsAg in sérum prior to administration of the first dose of the protein based vaccine. In certain embodiments, the subject has an HBsAg of 2 log 10 lU/ml or less in sérum prior to administration of the vaccine.
In certain embodiments, the RNAi agent is administered to the subject no more than once per week. In certain embodiments, the RNAi agent is administered to the subject no more than once every four weeks.
In certain embodiments, the RNAi ageint is administered to the subject at a dose of 0.01 mg/kg to 10 mg/kg; or 0.5 mg/kg to 50 mg/kg; or 10 mg/kg to 30 mg/kg. In certain embodiments, the RNAi agent is administered to the subject at a dose selected from 0.5 mg/kg, 1 mg/kg, 1.5 mg/kg, 3 mg/kg, 5 mg/kg, 10 mg/kg, and 30 mg/kg. In some embodiments, a dose of the RNAi agent is administered to the subject about once per week; about one every two weeks; about once every three weeks; about once every four weeks; or a dose of the RNAi agent is administered to the subject not more than once per week; or a dose of the RNAi agent is administered to the subject no more than once every four weeks.
In certain embodiments, the protein-based vaccine comprises an amino acid sequence of at least one déterminant of HBsAg and at least one déterminant of HBcAg.
In certain embodiments, the nucleic acid-based vaccine comprising an expression vector construct encoding an HBcAg or an HBsAg encodes an amino acid sequence comprising at least one déterminant of HBsAg or at least one déterminant of HBcAg
In certain embodiments, the déterminant of HBsAg comprises a sequence at least 90% identical to amino acids 124 to 147 of SEQ ID NO: 22. In certain embodiments, the déterminant of HBsAg comprises a sequence at least 90% identical to amino acids 99 to 168 of SEQ ID NO: 23.
In certain embodiments, the déterminant of HBcAg comprises a sequence comprising amino acid 80 of SEQ ID NO: 24. In certain embodiments, the sequence comprising amino acid 80 of SEQ ID NO: 24 comprises an amino acid sequence at lest 90% identical to at least amino acids 70 to 90 of SEQ ID NO: 24. In certain embodiments, the déterminant of HBcAg comprises a sequence comprising amino acid 138 of SEQ ID NO: 24. In certain embodiments, the sequence comprising
amino acid 80 of SEQ ID NO: 14 comprises an amino acid sequence at lest 90% identical to at least amino acids 128 to 143 of SEQ ID NO: 24. In certain embodiments, the déterminant of HBcAg comprises an amino acid sequence at least 90% identical to at least 40,50,60,70, 80,90, or 100 contiguous amino acids of SEQ ID NO: 24. In certain embodiments, the déterminant of HBcAg comprises a sequence at least 90% identical to amino acids 18 to 143 of SEQ ID NO: 24.
In certain embodiments, the protein-based vaccine administered to the subject comprises a dose of 0.1 pg to 1.0 mg of the HBcAg and a dose of 0.1 pg to 1.0 mg of HBsAg. In some embodiments, a dose of the protein-based vaccine is administered to the subject about once per week; about one every two weeks; about once every three weeks; about once every four weeks; or a dose of the protein-based vaccine is administered to the subject no more than once per week; or a dose of the protein-based vaccine is administered to the subject no more than once every four weeks.
In certain embodiments, the HBcAg protein and the HBsAg protein are présent in a single formulation. In certain embodiments, the HBcAg protein and the HBsAg protein are not présent in a single formulation. In certain embodiments, the protein-based vaccine comprises an adjuvant. In some embodiments, the adjuvant stimulâtes a balanced Thl/Th2 response. In certain embodiments, the adjuvant is selected from monophosphoryl lipid A (MPL), poly(I:C), polyICLC adjuvant, CpG DNA, polyICLC adjuvant ,a STING agonist, c-di-AMP, c-di-GMP, c-di-CMP; short, blunt-ended 5 triphosphate dsRNA (3pRNA) Rig-Iligand, poly[di(sodiumcarboxylatoethylphenoxy)phosphazene] (PCEP)), alum, virosomes, cytokines, IL-12, AS02, AS03, AS04, MF59, ISCOMATRIX®, IC31®, or Rig-I ligand. In certain embodiments, the adjuvant is selected from polyI:C adjuvant, a CpG adjuvant, a STING agonist, or a PCEP adjuvant.
In certain embodiments, the protein based vaccine is administered to the subject at least two times. In certain embodiments, the protein-based vaccine is administered to the subject no more than once every two weeks. In certain embodiments, the protein-based vaccine is administered to the subject no sooner than the day on which the final dose of the RNAi agent has been administered to the subject. In certain embodiments, the protein-based vaccine is administered to the subject on the same day on which the final dose of the RNAi agent has been administered to the subject. In certain embodiments, the protein based vaccine is administered to the subject no later than one month after the final dose of the RNAi agent has been administered to the subject. In certain embodiments, the protein based vaccine is administered to the subject no later than two months after the final dose of the RNAi agent has been administered to the subject. In certain embodiments, the protein based vaccine is administered to the subject no later than three months after the final dose of the RNAi agent has been administered to the subject.
In certain embodiments the methods of the invention further comprise determining the sérum HBsAg level after administration of at least one dose of the RNAi agent and prior to administration of the protein based vaccine. That is, the sérum HBsAg level is determined in the subject after administration of at least one dose of the RNAi agent and prior to administration of the protein based vaccine.
In certain embodiments the methods of the invention further comprise determining the sérum HBeAg level after administration of at least one dose of the RNAi agent and prior to administration of the protein based vaccine. That is, the sérum HBeAg level is determined in the subject after administration of at least one dose of the RNAi agent and prior to administration of the protein based 5 vaccine.
In certain embodiments the methods of the invention further comprise determining the sérum HBsAg level and the HBeAg level after administration of at least one dose of the RNAi agent and prior to administration of the protein based vaccine. That is, the sérum HBsAg level and the sérum HBeAg level are determined in the subject after administration of at least one dose of the RNAi agent 10 and prior to administration of the protein based vaccine.
In certain embodiments, the nucleic acid-based vaccine comprises at least one expression vector construct encoding both an HBeAg and an HBsAg. In certain embodiments, the expression construct promotes expression of HBeAg and HBsAg from a single promoter. In other embodiments, the expression construct promotes expression of HBeAg and HBsAg from separate promoters.
In certain embodiments, at least one promoter is selected from a respiratory syncytial virus (RSV) promoter, a cytomégalovirus (CMV) promoter, a PH5 promoter, and an H1 promoter. In certain embodiments, the expression construct comprises a viral vector. In certain embodiments, the viral vector is selected from adenovirus vector; retrovirus vector, lentiviral vector, moloney murine leukemia virus vector, adeno- associated virus vector; herpes simplex virus vector, SV 40 vector;
polyoma virus vector; papilloma virus vector; picomavirus vector; pox virus vector, orthopox virus vector, vaccinia virus vector, modified vaccinia virus Ankara (MVA) vector, avipox vector, canary pox vector, fowl pox vector, adenovirus vector, and Epstein Barr virus vector. In certain embodiments, the viral vector is an MVA vector.
In certain emboidments, the nucleic acid-based vaccine administered to the subject comprises 25 a tissue-culture infectious dose (TCID50) of 106 to 1010 TCID50; or 106 to 10’ TCID50; or 106 to 108 TCID50
In certain embodiments, the nucleic acid-based vector is administered to the subject no sooner than two weeks after administration of the final dose of the protein-based vaccine is administered to the subject.
In certain embodiments, the methods further comprise determining the sérum HBsAg level after administration of at least one dose of the RNAi agent and prior to administration of the nucleic acid-based vaccine. That is, the sérum HBsAg level is determined in the subject after administration of at least one dose of the RNAi agent and prior to administration of the nucleic acid-based vaccine. In certain embodiments, the nucleic acid-based vaccine is administered to the subject after a further decrease of at least 0.5 log 10 of sérum HBsAg after at least one dose of the protein-based vaccine is administered to the subject. In certain embodiments of the regimen, a single dose of the nucleic-acid based vaccine is administered to the subject.
In certain embodiments, the methods further comprise determining the sérum HBeAg level after administration of at least one dose of the RNAi agent and pnor to administration of the nucleic acid-based vaccine. That is, the sérum HBeAg level is determined in the subject after administration of at least one dose of the RNAi agent and prior to administration of the nucleic acid-based vaccine. In certain embodiments, the nucleic acid-based vaccine is administered to the subject after a further decrease of at least 0.5 log 10 of sérum HBeAg after at least one dose of the protein-based vaccine is administered to the subject. In certain embodiments of the regimen, a single dose of the nucleic-acid based vaccine is administered to the subject.
In certain embodiments, the methods further comprise determining the sérum HBsAg level and the HBeAg level after administration of at least one dose of the RNAi agent and prior to administration of the nucleic acid-based vaccine. That is, the sérum HBsAg level and the sérum HBeAg level are determined in the subject after administration of at least one dose of the RNAi agent and prior to administration of the nucleic acid-based vaccine. In certain embodiments, the nucleic acid-based vaccine is administered to the subject after a further decrease of at least 0.5 log 10 of sérum HBsAg and sérum HBeAg after at least one dose of the protein-based vaccine is administered to the subject. In certain embodiments of the regimen, a single dose of the nucleic-acid based vaccine is administered to the subject.
In certain embodiments, the methods further comprise administering a nucleot(s)ide analog to the subject at least prior to administration of the iRNA targeted to HBV. In certain embodiments, the nucleot(s)ide analog is administered throughout the entire regimen. In certain embodiments, the nucleot(s)ide analog is selected from Tenofovir disoproxil fumarate (TDF), Tenofovir alafenamide (TAF), Lamivudine, Adefovir dipivoxil, Entecavir (ETV), Telbivudine, AGX-1009, emtricitabine, clevudine, ritonavir, dipivoxil, lobucavir, famvir, FTC, N-Acetyl-Cysteine (NAC), PC 1323, theradigm-HBV, thymosin-alpha, and ganciclovir, besifovir (ANA-380/LB-80380), and tenofovirexaliades (TLX/CMX157).
In certain embodiments, the subject has sérum HBsAg below 3000 lU/ml prior to administration of the RNAi agent. In certain embodiments, the subject has sérum HBsAg below 4000 lU/ml prior to administration of the RNAi agent. In certain embodiments, subject has sérum HBsAg below 5000 lU/ml prior to administration of the RNAi agent.
In certain embodiments, the subject has a réduction of HBsAg level of at least 2 logio scales after administration of the RNAi agent and prior to administration of the first dose of a protein-based vaccine. In certain embodiments, the subject has a réduction of HBeAg level of at least 1 logio scale after administration of the RNAi agent and prior to administration of the first dose of a protein-based vaccine. In certain embodiments, the subject has a réduction of HBsAg level of at least 2 logio scales and a réduction of HBeAg level of at least 1 logio scale after administration of the RNAi agent and prior to administration of the first dose of a protein-based vaccine.
In certain embodiments, the subject has a réduction of HBsAg level to 500 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based
vaccine. In certain embodiments, the subject has a réduction of HBsAg level to 200 lU/ml or less after administration of the RNAi agent and pnor to administration of a first dose of the protein based vaccine. In certain embodiments, the subject has a réduction of HBsAg level to 100 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based vaccine.
In certain embodiments, the subject has a réduction of HBeAg level to 500 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based vaccine. In certain embodiments, the subject has a réduction of HBeAg level to 200 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based vaccine. In certain embodiments, the subject has a réduction of HBeAg level to 100 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based vaccine.
In certain embodiments, the subject has a réduction of HBsAg level and HBeAg level to 500 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based vaccine. In certain embodiments, the subject has a réduction of HBsAg level and HBeAg level to 200 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based vaccine. In certain embodiments, the subject has a réduction of HBsAg level and HBeAg level to 100 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein based vaccine.
In certain embodiments, the level of sérum HBsAg and HBeAg in the subject are decreased to below the level of détection using a clinical assay for at least three months after the end of the dose of the nucleic acid-based vaccine. In certain embodiments, the level of sérum HBsAg and HBeAg in the subject are decreased to below the level of détection using a clinical assay for at least six months after the end of the dose of the nucleic acid-based vaccine.
In certain embodiments, sérum HBsAg in the subject is decreased to below the level of détection using a clinical assay for at least six months after the end of the dose of the nucleic acidbased vaccine.
In certain embodiments, the methods further comprise administration of an immune stimulator to the subject. In certain embodiments, the immune stimulator is selected from the group pegylated interferon alfa 2a (PEG-IFN-alpha-2a), Interferon alfa-2b, PEG-IFN-aIpha-2b, Interferon lambda a recombinant human interleukin-7, and a Toll-like receptor 3,7, 8 or 9 (TLR3, TLR7, TLR8, TLR9) agonist, a viral entry inhibitor, Myrcludex, an oligonucleotide that inhibits the sécrétion or release of HBsAg, REP 9AC, a capsid inhibitor, Bay41-4109, NVR-1221, a cccDNA inhibitor, IHVR-25) a viral capsid, an MVA capsid, an immune checkpoint regulator, an CTLA-4 inhibitor, ipilimumab, a PD-1 inhibitor, Nivolumab, Pembrolizumab, BGB-A317 antibody, a PD-L1 inhibitor, atezolizumab, avelumab, durvalumab, and an afïimer biotherapeutic.
In certain embodiments of the regimen, the subject is human.
In certain embodiments of the regimen, the RNAi agent targets four transcripts of HBV. In certain embodiments, the RNAi agent is selected from an iRNA in Appendix A. In certain embodiments, the RNAi agent is selected from any of the agents in any one of Tables 2-11 in Appendix A. In certain embodiments, the RNAi agent targets at least 15 contiguous nucléotides of 5 nucléotides 206-228,207-229, 210-232, 212-234,214-236,215-237,216-238, 226-248, 245-267, 250-272, 252-274, 253-275, 254-276,256-278,258-280, 263-285, 370-392, 373-395, 375-397,401423,405-427,410-432,411-433,422-444,424-446,425-447,426-448, 731-753,734-756, 11741196,1250-1272,1255-1277, 1256-1278,1545-1567,1547-1569, 1551-1571,1577-1597, 1579-1597, 1580-1598, 1806-1825, 1812-1831, 1814-1836, 1829-1851, 1831-1853, 1857-1879, 1864-1886,225910 2281,2298-2320, or 2828-2850 of SEQID NO: 1 (NC_003977.1). In certain embodiments, the
RNAi agent targets at least 15 contiguous nucléotides of nucléotides 1579-1597 or 1812-1831 of SEQ ID NO: 1 (NC_003977.1). In certain embodiments, the RNAi agent targets nucléotides 1579-1597 or 1812-1831 ofSEQIDNO: 1 (NC 003977.1).
In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide 15 sequence of at least 15 contiguous nucléotides ofUGUGAAGCGAAGUGCACACUU (SEQ ID NO:
25) or AGGUGAAAAAGUUGCAUGGUGUU (SEQ ID NO: 26). In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide sequence of at least 19 contiguous nucléotides of UGUGAAGCGAAGUGCACACUU (SEQ ID NO: 25) or AGGUGAAAAAGUUGCAUGGUGUU (SEQ ID NO: 26). In certain embodiments, the antisense 20 strand of the RNAi agent comprises a nucléotide sequence of UGUGAAGCGAAGUGCACACUU (SEQ ID NO: 25) or AGGUGAAAAAGUUGCAUGGUGUU (SEQ ID NO: 26).
In certain embodiments, the sense strand of the RNAi agent comprises a nucléotide sequence of at least 15 contiguous nucléotides of GUGUGCACUUCGCUUCACA (SEQ ID NO: 27) or CACCAUGCAACUUUUUCACCU (SEQ ID NO: 28). In certain embodiments, the sense strand of 25 the RNAi agent comprises a nucléotide sequence of at least 19 contiguous nucléotides of
GUGUGCACUUCGCUUCACA (SEQ ID NO: 27) or CACCAUGCAACUUUUUCACCU (SEQ ID NO: 28). In certain embodiments, the sense strand of the RNAi agent comprises a nucléotide sequence of GUGUGCACUUCGCUUCACA (SEQ ID NO: 27) or CACCAUGCAACUUUUUCACCU (SEQ ID NO: 28).
In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide sequence of at least 15 contiguous nucléotides of UGUGAAGCGAAGUGCACACUU (SEQ ID NO: 25) and the sense strand comprises a nucléotide sequence of at least 15 contiguous nucléotides of GUGUGCACUUCGCUUCACA (SEQ ID NO: 27). In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide sequence of at least 19 contiguous nucléotides of
UGUGAAGCGAAGUGCACACUU (SEQ ID NO: 25) and the sense strand comprises a nucléotide sequence of at least 19 contiguous nucléotides of GUGUGCACUUCGCUUCACA (SEQ ID NO: 27). In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide sequence of
UGUGAAGCGAAGUGCACACUU (SEQ ID NO: 25) and the sense strand comprises a nucléotide sequence of GUGUGCACUUCGCUUCACA (SEQ ID NO: 27).
In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide sequence of at least 15 contiguous nucléotides of AGGUGAAAAAGUUGCAUGGUGUU (SEQ ID NO: 26) and the sense strand of the RNAi agent comprises a nucléotide sequence of at least 15 contiguous nucléotides of CACCAUGCAACUUUUUCACCU (SEQ ID NO: 28). In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide sequence of at least 19 contiguous nucléotides of AGGUGAAAAAGUUGCAUGGUGUU (SEQ ID NO: 26) and the sense strand of the RNAi agent comprises a nucléotide sequence of at least 19 contiguous nucléotides of CACCAUGCAACUUUUUCACCU (SEQ ID NO: 28). In certain embodiments, the antisense strand of the RNAi agent comprises a nucléotide sequence of AGGUGAAAAAGUUGCAUGGUGUU (SEQ ID NO: 26) and the sense strand of the RNAi agent comprises a nucléotide sequence of CACCAUGCAACUUUUUCACCU (SEQ ID NO: 28).
In certain embodiments of the regimen, substantially ail of the nucléotides of said sense strand and substantially ail of the nucléotides of said antisense strand are modified nucléotides, wherein said sense strand is conjugated to a ligand attached at the 3’-terminus. In certain embodiments, the ligand is one or more GalNAc dérivatives attached through a monovalent linker, bivalent branched linker, or trivalent branched linker. In certain embodiments, the at least one of said modified nucléotides is selected from the group consisting of a deoxy-nucleotide, a 3’-terminal deoxy-thymine (dT) nucléotide, a 2'-O-methyl modified nucléotide, a 2'-fluoro modified nucléotide, a 2'-deoxy-modifïed nucléotide, a locked nucléotide, an unlocked nucléotide, a conformationally restricted nucléotide, a constrained ethyl nucléotide, an abasic nucléotide, a 2’-amino-modified nucléotide, a 2’-O-allylmodified nucléotide, 2’-C-alkyl-modified nucléotide, 2’-hydroxly-modified nucléotide, a 2’methoxyethyl modified nucléotide, a 2’-O-alkyl-modified nucléotide, a morpholino nucléotide, a phosphoramidate, a non-natural base comprising nucléotide, a tetrahydropyran modified nucléotide, a 1,5-anhydrohexitol modified nucléotide, a cyclohexenyl modified nucléotide, a nucléotide comprising a phosphorothioate group, a nucléotide comprising a methylphosphonate group, a nucléotide comprising a 5’-phosphate, and a nucléotide comprising a 5’-phosphate mimic.
In certain embodiments, at least one strand of the RNAi agent comprises a 3’ overhang of at least 1 nucléotide. In certain embodiments, at least one strand if the RNAi agent comprises a 3’ overhang of at least 2 nucléotides. In certain embodiments, the double-stranded région of the RNAi agent is 15-30 nucléotide pairs in length; 17-23 nucléotide pairs in length; 17-25 nucléotide pairs in length; 23-27 nucléotide pairs in length; 19-21 nucléotide pairs in length; 21-23 nucléotide pairs in length.
In certain embodiments, each strand of the RNAi agent has 15-30 nucléotides.
In certain embodiments, each strand of the RNAi agent has 19-30 nucléotides.
In certain embodiments, the ligand is
and the RNAi agent is optionally conjugated to the ligand as shown in the following schematic
3*
wherein X is O or S.
In certain embodiments, the sense strand comprises the nucléotide sequence 5’gsusguGfcAfCfUfiicgcuucaca-3’ (SEQID NO: 29) and the antisense strand comprises the nucléotide sequence 5’-usGfsugaAfgCfGfaaguGfcAfcacsusu-3’ (SEQ ID NO: 30); or the sense strand comprises the nucléotide sequence 5’-csasccauGfcAfAfCfuuuuucaccu-3’ (SEQ ID NO: 31) and the antisense strand comprises the nucléotide sequence 5’-asGfsgugAfaAfAfaguuGfcAfuggugsusu-3’ (SEQ ID NO: 32), wherein a, c, and u are 2'-O-methyladenosine-3’-phosphate, 2'-O-methyIcytidine3’-phosphate, and 2'-O-methyluridine-3’-phosphate, respectively; as, es, gs, and us are 2'-Omethyladenosine-3’- phosphorothioate, 2'-O-methylcytidine-3’- phosphorothioate, 2'-Omethylguanosine-3’- phosphorothioate, and 2'-O-methyluridine-3’-phosphorothioate, respectively; Af,
Cf, Gf, and Uf are 2’-fluoroadenosine-3’-phosphate, 2’-fluorocytidine-3’-phosphate, 2’fluoroguanosine-3’-phosphate, and 2’-fluorouridine-3’-phosphate, respectively; and Gfs is 2’fluoroguanosine-3’-phosphorothioate. In certain embodiments, the RNAi agent is AD-66810 or AD66816.
In certain embodiments, the protein-based vaccine comprises epitopes présent in at least 4,5, 20 6, 7, 8, 9, or 10 génotypes of HBV.
In certain embodiments, the nucleic acid-based vaccine comprises epitopes présent in at least 4, 5, 6, 7, 8, 9, or 10 génotypes of HBV.
The présent invention further provides uses of the RNAi agents and vaccines provided herein for treatment of subjects having a hepatitis B virus infection based on the methods provided herein. In certain embodiment, the RNAi agents and the HBV vaccines are used in the manufacture of médicaments for treatment of a subject with an HBV infection.
The présent invention further provides kits comprising RNAi agents and vaccines provided herein and instructions providing treatment regimens for their use for treatment of subjects having a hepatitis B virus infection.
The présent invention is further illustrated by the following detailed description and drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 schematically depicts the structure of the approximately 3.2 kb double-stranded HBV genome. Réplication of the HBV genome occurs through an RNA intermediate and produces 4 overlapping viral transcripts of about 3.5 kb, 2.4 kb, 2.1 kb, and 0.7 kb (termination sites indicated by arrows), and the common 3’ end encoding seven viral proteins (pre-Sl, pre-S2, S, P, X, pre-C, and C) that are translated across three reading frames.
Figures 2A-2E are graphs showing suppression of HBV by siRNA in a transgenic mouse model. The level of (2A) HBsAg, (2B) HBeAg, and (2C) HBV-DNA in sérum of HBV1.3-xfs mice (n = 6 per group) after a single subcutaneous 3 mg/kg or 9 mg/kg dose of a control GalNAc-siRNA (an siRNA that does not target HBV), AD-66816, or AD-66810. The level of (2D) total HBV RNA and (2E) 3.5 kb HBV transcripts from liver lysâtes determined via RT-qPCR and normalized to expression of Glyceraldehyde 3-phosphate dehydrogenase (GAPDH).
Figure 3 is a schematic showing a dosing regimen for an experiment assaying the effect of pretreatment of HBV1.3-xfs mice with the nucleoside inhibitor, Entecavir, an HBV-shRNA, a control GalNAc-siRNA, AD-66816, or AD-66810 prior to administration of a therapeutic vaccine against HBV.
Figures 4A-4C are graphs showing the level of (4A) HBsAg, (4B) HBeAg, and (4C) HBVDNA in sérum of HBV1.3-xfs mice after treatment based on the dosing regimen provided in Figure 3.
Figures 5A-5F are graphs showing T cell immune response in the liver against peptides (5A) HBs(S208), (5B) HBc(C93), and (5C) MVA(B8R) in HBV1.3-xfs mice after treatment based on the dosing regimen provided in Figure 3. Figures 5D-5F show a reanalysis of the same data in Figures 5A-5C performed to accommodate for an insufficient exclusion of dead immune cells and shows T cell immune response in the liver against peptides (5D) HBs(S208), (5E) HBc(C93), and (5F) MVA(B8R).
Figures 6A-6C show the level of HBV RNA and protein levels in liver cells in HBV1.3-xfs mice after treatment based on the dosing regimen provided in Figure 3. Figure 6A shows total HBV RNA. Figure 6B shows HBV 3.5 kb transcript relative to GAPDH as determined by RT-qPCR. Figure 6C shows the number of HBcAg positive cells per mm2 of liver section detected by immunohistochemical staining.
Figure 7 is a schematic showing a dosing regimen for the experiment assaying the effect of pretreatment of HBV1.3-xfs mice with control siRNA or AD-66816 prior to administration of a therapeutic vaccine against HBV.
Figures 8A-8C are graphs showing the level of (8A) HBsAg, (8B) HBeAg, and (8C) HBVDNA in sérum of HBV1.3-xfs mice after treatment based on the dosing regimen provided in Figure 7.
Figures 9A-9D are graphs showing T cell immune response in the liver against peptides (9A) HBs(S208), (9B) HBc(C93), (9C) HBc(Cpool) and (9D) MVA(B8R) in HBV1.3-xfs micfe after treatment based on the dosing regimen provided in Figure 7.
Figures 10A-10C show the level of HBV RNA and protein levels in liver cells of HBV1.3-xfs mice after treatment based on the dosing regimen provided in Figure 7. Figure 10A shows total HBV RNA. Figure 10B shows HBV 3.5 kb transcript relative to GAPDH as determined by RT-qPCR. Figure 10C shows the number of HBcAg positive cells per mm2 of liver section detected by immunohistochemical staining.
Figures 1 IA and 1 IB are graphs showing the level of (1 IA) HBsAg and (1 IB) HBeAg in sérum of individual HBV1.3-xfs mice at week 7 after the first vaccine dose after the 6 week regimen in the dosing regimen provided in Figure 7.
Figures 1 IC and 1 ID are graphs showing (1 IC) anti-HBs antibody response and (1 ID) T cell immune response in the liver against HBs(S208) of individual HBV1.3-xfs mice at week 7 after the first vaccine dose after the 6 week regimen in the dosing regimen provided in Figure 7.
Figure 12 is a schematic showing a dosing regimen for the experiment assaying the effect of pretreatment of mice infected with an AAV vector encoding HBV with control siRNA or AD-66816 prior to administration of a therapeutic vaccine against HBV.
Figures 13A-13G are based on the dosing regimen provided in Figure 12. Figures 13A and 13B are graphs showing the level of (13A) HBsAg and (13B) HBeAg in sérum of HBV-AAV mice (inset 13C is an exploded portion of the later time points in graph 13B). Figure 13D shows the sérum HBV DNA level at week 22. Figures 13D and 13E show the number of copies per liver cell of (13D) total HBV DNA and (13E) AAV-DNA at week 22. Figures 13F and 13G show the relative expression in liver of (13F) HBV 3.5 RNA relative to GAPDH RNA and (13G) total HBV RNA relative to GAPDH RNA.
Figures 14A-14C are graphs showing (14A) anti-HBs antibody response throughout the course of the experiment and (14B) anti-HBe antibody response at day 116 of the experiment based on the dosing regimen provided in Figure 12. Figure 14C is an exploded portion of the later time points in graph 14B.
Figures 15A and 15B show (15A) ALT levels and (15B) body weights of the animais throughout the experiment based on the dosing regimen provided in Figure 12.
A formai sequence listing is provided herewith that forms part of the spécification.
An Appendix A providing exemplary target sequences for siRNA targeting and iRNA agents is provided herewith and forms part of the spécification.
DETAILED DESCRIPTION OF THE INVENTION
The présent invention provides treatment regimens and methods of use of iRNA agents which effect the RNA-induced silencing complex (RlSC)-mediated cleavage of RNA transcripts of one or more HBV genes (open reading frames/ transcripts) and hepatitis B vaccines to stimulate an immune response against one or more HBV proteins in the treatment of HBV infection. The treatment regimens and methods preferably provide a functional cure within a defined period of time.
The following detailed description discloses how to make and use compositions containing iRNAs to inhibit the expression of an HBV gene as well as compositions, uses, and methods for treating subjects having diseases and disorders that would benefit from inhibition or réduction of the expression of an HBV gene.
I. Définitions
In order that the présent invention may be more readily understood, certain terms are first defined. In addition, it should be noted that whenever a value or range of values of a parameter are recited, it is intended that values and ranges intermediate to the recited values are also intended to be part of this invention.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element, e.g., a plurality of éléments.
The term including is used herein to mean, and is used interchangeably with, the phrase including but not limited to.
The term or is used herein to mean, and is used interchangeably with, the term and/or, unless context clearly indicates otherwise.
The term “about” is used herein to mean within the typical ranges of tolérances in the art. For example, “about” can be understood as within 2 standard déviations from the mean. In certain embodiments, “about” means +/-10%. In certain embodiments, “about” means +/-5%. When about is présent before a sériés of numbers or a range, it is understood that “about” can modify each of the numbers in the sériés or range.
The term “at least” prior to a number or sériés of numbers is understood to include the number adjacent to the term “at least”, and ail subséquent numbers or integers that could logically be included, as clear from context. For example, the number of nucléotides in a nucleic acid molécule must be an integer. For example, “at least 18 nucléotides of a 21 nucléotide nucleic acid molécule” means that 18,19,20, or 21 nucléotides hâve the indicated property. When at least is présent before a
sériés of numbers or a range, it is understood that “at least” can modify each of the numbers in the senes or range.
As used herein, “no more than” or “less than” is understood as the value adjacent to the phrase and logical lower values or integers, as logical from context, to zéro. For example, a duplex with an overhang of “no more than 2 nucléotides” has a 2, 1, or 0 nucléotide overhang. When “no more than” is présent before a sériés of numbers or a range, it is understood that “no more than” can modify each of the numbers in the sériés or range. As used herein, ranges include both the upper and lower limit.
In the event of a conflict between a sequence and its indicated site on a transcript or other sequence, the nucléotide sequence recited in the spécification takes precedence.
Various embodiments of the invention can be combined as determined appropriate by one of skill in the art. ’
As used herein, “Hepatitis B virus,” used interchangeably with the term “HBV” refers to the well-known non-cytopathic, liver-tropic DNA virus belonging to the Hepadnaviridae family.
The HBV genome is partially double-stranded, circular DNA with overlapping reading frames (see, e.g., Figure 1).
There are four transcripts (that may be referred to herein as “genes” or “open reading frames”) based on size, encoded by the HBV genome. These contain open reading frames called C, X, P, and S. The core protein is coded for by gene C (HBeAg). Hepatitis B e antigen (HBeAg) is produced by proteolytic processing of the pre-core (pre-C) protein. The DNA polymerase is encoded by gene P. Gene S is the gene that codes for the surface antigens (HBsAg). The HBsAg gene is one long open reading frame which contains three in frame start (ATG) codons resulting in polypeptides of three different sizes called large, middle, and small S antigens, pre-Sl + pre-S2 + S, pre-S2 + S, or S. Surface antigens in addition to decorating the envelope of HBV, are also part of subviral particles, which are produced at large excess as compared to virion particles, and play a rôle in immune tolérance and in sequestering anti-HBsAg antibodies, thereby allowing for infections particles to escape immune détection. The function of the non-structural protein coded for by gene X is not fully understood, but it plays a rôle in transcriptional transactivation and réplication and is associated with the development of liver cancer. Exemplary protein sequences are provided in the attached sequence listing (see, e.g., SEQID NOs:l, 3,16, and 20).
HBV is one of the few DNA viruses that utilize reverse transcriptase in the réplication process which involves multiple stages including entry, uncoating, ànd transport of the virus genome to the nucléus. Initially, réplication of the HBV genome involves the génération of an RNA intermediate that is then reverse transcribed to produce the DNA viral genome.
Upon infection of a cell with HBV, the viral genomic relaxed circular DNA (rcDNA) is transported into the cell nucléus and converted into episomal covalently closed circular DNA. (cccDNA), which serves as the transcription template for the viral mRNAs. After transcription and nuclear export, cytoplasmic viral pregenomic RNA (pgRNA) is assembled with HBV polymerase and
capsid proteins to form the nucleocapsid, inside which polymerase-catalyzed reverse transcription yields minus-strand DNA, which is subsequently copied into plus-strand DNA to form the progeny rcDNA genome. The mature nucleocapsids are then either packaged with viral envelope proteins to egress as virion particles or shuttled to the nucléus to amplify the cccDNA réservoir through the intracellular cccDNA amplification pathway. cccDNA is an essential component of the HBV réplication cycle and is responsible for the establishment of infection and viral persistence.
HBV infection results in the production of two different particles: 1 ) the infections HBV virus itself (or Dane particle) which includes a viral capsid assembled from the HBcAg and is covered by an envelope consisting of a lipid membrane with HBV surface antigens, and 2) subviral particles (or SVPs) which contain the small and medium forms of the hepatitis B surface antigen HBsAg which are non-infectious. For each viral particle produced, over 10,000 SVPs are released into the blood. As such, SVPs (and the HBsAg protein they carry) represent the overwhelming majority of viral protein in the blood. HBV infected cells also secrete a soluble proteolytic product of the pre-core protein called the HBV e-antigen (HBeAg).
Eight génotypes of HBV, designated A to H, hâve been determined, and two additional génotypes I and J hâve been proposée!, each having a distinct geographical distribution. The virus is non-cytopathic, with virus-specific cellular immunity being the main déterminant for the outcome of exposure to HBV- acute infection with resolution of liver diseases with 6 months, or chronic HBV infection that is frequently associated with progressive liver injury.
The term “HBV” includes any of the génotypes of HBV (A to J). The complété coding sequence of the reference sequence of the HBV genome may be found in for example, GenBank Accession Nos. GI:21326584 (SEQ ID NO:1) and GI:3582357 (SEQ ID NO:3). Antisense sequences are provided in SEQ ID NO: 2 and 4, respectively. Amino acid sequences for the C, X, P, and S proteins can be found, for example at NCBI Accession numbers YP_009173857.1 (C protein); YP_009173867.1 and BAA32912.1 (X protein); YP_009173866.1 andBAA32913.1 (P protein); and YP_009173869.1, YP_009173870.1, YP_009173871.1, and BAA32914.1 (S protein) (SEQ ID NOs: 5-13) . Protein and DNA sequences from HBV génotype D, strain ayw are provided in SEQ ID NOs.: 14-17. Protein and DNA sequences from HBV génotype A, strain adw are provided in SEQ ID NOs.: 18-21.
Additional examples of HBV mRNA sequences are readily available using publicly available databases, e.g., GenBank, UniProt, and OMIM. The International Repository for Hepatitis B Virus Strain Data can be accessed at http://www.hpa-bioinformatics.org.uk/HepSEQ/main.php.
The term “HBV,” as used herein, also refers to naturally occurring DNA sequence variations of the HBV genome, i.e., génotypes A-J and variants thereof.
As used herein, “epitope” also referred to as “an antigenic déterminant,” or “déterminant,” is understood as the part of a protein antigen that is recognized by the immune system, specifîcally by antibodies, B cells, and/or T cells. Epitopes include conformational epitopes and linear epitopes. Proteins share an epitope when they share an amino acid sequence of sufficient length or size and
antigenicity to be recognized by an antibody, B cell, and/or T cell. T cell epitopes presented by MHC class I molécules are typically peptides about 8 to 11 amino acids m length, whereas MHC class Π molécules présent longer peptides about 13 to 17 amino acids in length. Conformational epitopes are typically discontinuons and span a longer amino acid sequence.
As used herein, the term “nucelot(s)ide analog” or “reverse transcriptase inhibitor” is an inhibitor of DNA réplication that is structurally similar to a nucléotide or nucleoside and specifically inhibits réplication of the HBV cccDNA and does not significantly inhibit the réplication of the host (e.g., human) DNA. Such inhibitors include Tenofovir disoproxil fumarate (TDF), Tenofovir alafenamide (TAF), Lamivudine, Adefovir dipivoxil, Entecavir (ETV), Telbivudine, AGX-1009, emtricitabine, clevudine, ritonavir, dipivoxil, lobucavir, famvir, FTC, N-Acetyl-Cysteine (NAC), PC1323, theradigm-HBV, thymosin-alpha, ganciclovir, besifovir (ANA-380/LB-80380), and tenofvirexaliades (TLX/CMX157). In certain embodiments, the nucelot(s)ide analog is Entecavir (ETV). Nucleot(s)ide analogs are commercially available from a number of sources and are used in the methods provided herein according to their label indication (e.g., typically orally administered at a spécifie dose) or as determined by a skilled practitioner in the treatment of HBV.
As used herein, “target sequence” refers to a contiguous portion of the nucléotide sequence of an mRNA molécule formed during the transcription of an HBV transcript, including mRNA that is a product of RNA processing of a primary transcription product. In one embodment, the target portion of the sequence will be at least long enough to serve as a substrate for iRNA-directed cleavage at or near that portion of the nucléotide sequence of an mRNA molécule formed during the transcription of an HBV transcript. In one embodiment, the target sequence is within the protein coding région of an HBV transcript.
The target sequence may be from about 9-36 nucléotides in length, e.g., about 15-30 nucléotides in length. For example, the target sequence can be from about 15-30 nucléotides, 15-29, 15-28, 15-27, 15-26, 15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30, 18-29, 1828, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30, 19-29, 19-28,19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20,20-30,20-29,20-28,20-27, 20-26,20-25,20-24,20-23, 20-22, 2021, 21-30,21-29,21-28,21-27,21-26,21-25,21-24, 21-23, or 21-22 nucléotides in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the invention.
As used herein, the term “strand comprising a sequence” refers to an oligonucleotide comprising a chain of nucléotides that is described by the sequence referred to using the standard nucléotide nomenclature.
“G,” “C,” “A,” “T,” and “U” each generally stand for a nucléotide that contains guanine, cytosine, adenine, thymidine, and uracil as a base, respectively. However, it will be understood that the term “ribonucleotide” or “nucléotide” can also refer to a modified nucléotide, as further detailed below, or a surrogate replacement moiety. The skilled person is well aware that guanine, cytosine, adenine, and uracil can be replaced by other moieties without substantially altering the base pairing
properties of an oligonucleotide comprising a nucléotide bearing such replacement moiety. For example, without limitation, a nucléotide comprising inosine as its base can base pair with nucléotides containing adenine, cytosine, or uracil. Hence, nucléotides containing uracil, guanine, or adenine can be replaced in the nucléotide sequences of dsRNA featured in the invention by a nucléotide containing, for example, inosine. In another example, adenine and cytosine anywhere in the oligonucleotide can be replaced with guanine and uracil, respectively to form G-U Wobble base pairing with the target niRNA. Sequences containing such replacement moieties are suitable for the compositions and methods featured in the invention.
As used herein, an “RNAi agent”, an “iRNA agent”, an “siRNA agent”, and the like, is a double stranded RNA that preferably target régions in the HBV genome that are conserved across ail serotypes of HBV and are preferably designed to inhibit ail steps of the HBV life cycle, e.g., réplication, assembly, sécrétion of virus, and sécrétion of viral antigens, by inhibiting expression of more than one HBV transcript. In particular, since transcription of the HBV genome results in polycistronic, overlapping RNAs, an RNAi agent for use in the invention targeting a single HBV transcript preferably results in significant inhibition of expression of most or ail HBV transcripts. Ail HBV transcripts are at least partly overlapping and share the same polyadenylation signal. Therefore, ail viral transcripts hâve an identical 3 'end and, thus, an RNAi agent of the invention targeting the X gene will target ail viral transcripts and should resuit in inhibition of not only X gene expression but also the expression of ail other viral transcripts, including pregenomic RNA (pgRNA). Furthermore, the RNAi agents of the invention hâve been designed to inhibit HBV viral réplication by targeting pgRNA, HBV structural genes, polymerase, and the HBV X gene. In addition, they hâve been designed to médiate the silencing of SVP and other viral protiens that play a rôle in immune tolérance, thereby permitting a subject’s immune system to detect and respond to the presence of viral antigens such that an immune response to control and to clear an HBV infection is mounted. Without intending to be limited by theory, it is believed that a combination or sub-combination of the foregoing properties and the spécifie target sites and/or the spécifie modifications in these RNAi agents confer to the RNAi agents of the invention improved efficacy, stability, safety, potency, and durability. Such agents are provided, for example, in PCT Publication Nos. WO 2016/077321, WO 2012/024170, WO 2017/027350, and WO 2013/003520, the entire contents of each of which is incorporated herein by reference. Exemplary target sites for RNAi agents and exemplary RNAi agents are provided in Appendix A, filed herewith, which forms a part of the spécification. The terni RNAi agents further includes shRNAs, e.g., adeno-associated virus (AAV) 8 vectors for delivery of an shRNA in an artificial mi(cro)RNA under a liver-specific promoter; optionally co-delivered a decoy (“TuD”) directed against the shRNA sense strand to curb off-target gene régulation are provided in Michler et al., 2016 (EMBO Mol. Med., 8:1082-1098, incorporated herein by reference).
The majority of nucléotides of each strand of an iRNA agent may be ribonucleotides, but as described in detail herein, each or both strands can also include one or more non-ribonucleotides, e.g., a deoxyribonucleotide and/or a modified nucléotide. In addition, as used in this spécification, an
“RNAi agent” may include ribonucleotides with Chemical modifications; an RNAi agent may include substantial modifications at multiple nucléotides.
As used herein, the term “modified nucléotide” refers to a nucléotide having, independently, a modified sugar moiety, a modified intemucleotide linkage, and/or modified nucleobase. Thus, the term modified nucléotide encompasses substitutions, additions or removal of, e.g., a functional group or atom, to intemucleoside linkages, sugar moieties, or nucleobases. The modifications suitable for use in the agents of the invention include ail types of modifications disclosed herein or known in the art. Any such modifications, as used in a siRNA type molécule, are encompassed by “RNAi agent” for the purposes of this spécification and claims.
As used herein, a “therapeutic HBV vaccine,” and the like, can be a peptide vaccine, a DNA vaccine including a vector-based vaccine, or a cell-based vaccine that induces an immune response, . preferably an effector T cell induced response, against one or more HBV proteins. Preferably the vaccine is a multi-epitope vaccine that is cross-reactive with multiple HBV serotypes, preferably ail HBV serotypes. A number of therapeutic HBV vaccines are known in the art and are at various stages of pre-clinical and clinical development. Protein based vaccines include hepatitis B surface antigen (HBsAg) and core antigen (HBcAg) vaccines (e.g., Li et al., 2015, Vaccine. 33:4247-4254, incorporated herein by reference). Exemplary DNA vaccines include HB-110 (Genexine, Kim et al., 2008. Exp Mol Med. 40: 669-676.), pDPSC18 (PowderMed), INO-1800 (Inovio Pharmaceuticals), HB02 VAC-AND (ANRS), and CVI-HBV-002 (CHA Vaccine Institute Co., Ltd.). Exemplary protein based vaccines include Theravax/DV-601 (Dynavax Technologies Corp.), εΡΑ-44 (Chongqing Jiachen Biotechnology Ltd.), and ABX 203 (ABIVAX S.A.). Exemplary cell based vaccines include HPDCs-T immune therapy (Sun Yat-Sen University). Combination vaccines and products are also known and include HepTcell™ (FP-02.2 vaccine (peptide) + IC31® Adjuvant (a combination peptide-oligonucleotide adjuvant),(see U.S. Patent Publication Nos. 2013/0330382,
2012/0276138, and 2015/0216967, the entire contents of each of which is incorporated herein by reference)); GS-4774 (Gilead, a fusion protein S. core X vaccine + Tarmogen T cell immune stimulator), pSG2.HBs/MVA.HBs (protein prime/viral vector boost, Oxxon Therapeutics), and a protein-prime/modified vaccinia virus Ankara vector-boost (HBsAg and HBsAg protein + HBcAg and HBsAg in MVA expression vector, Backes et al., 2016, Vaccine. 34:923-32, and
WO2017121791, both of which are incorporated herein by reference).
As used herein, the term “adjuvant” is understood to be an agent that promotes (e.g., enhances, accelerates, or prolongs) an immune response to an antigen with which it is administered to elicit long-term protective immunity. No substantial immune response is directed at the adjuvant itself. Adjuvants include, but are not limited to, pathogen components, particulate adjuvants, and combination adjuvants (see, e.g., www.niaid.nih.gov/research/vaccine-adjuvants-types). Pathogen components (e.g., monophosphoryl lipid A (MPL), poly(I:C), polyICLC adjuvant, CpG DNA, c-diAMP, c-di-GMP, c-di-CMP; short, blunt-ended 5'-triphosphate dsRNA (3pRNA) RIG-1 ligand, and émulsions such as poly[di(sodiumcarboxylatoethylphenoxy)phosphazene] (PCEP)) can help trigger
early non-specifïc, or innate, immune responses to vaccines by targeting various receptors inside or on the surface of innate immune cells. The innate immune system influences adaptive immune responses, which provide long-lasting protection against the pathogen that the vaccine targets. Particulate adjuvants (e.g., alum, virosomes, cytokines, e.g., IL-12) form very small particles that can stimulate 5 the immune system and also may enhance delivery of antigen to immune cells. Combination adjuvants (e.g., AS02, AS03, and AS04 (ail GSK); MF59 (Novartis); ISCOMATRIX® (CSL Limited); and IC31® (Altimmune) elicit multiple protective immune responses. Adjuvants that hâve a modest effect when used alone may induce a more potent immune response when used together.
In preferred embodiments of the invention, adjuvants for use in the invention promote a 10 humoral as well as a cellular immune response. For this, a balanced Thl/Th2 helper T cell response is desired to support neutralizing antibody responses as well as effector cytotoxic T cell responses. Preferably the adjuvant provides a balanced Thl/Th2 response. In certain embodiments, the adjuvant is one or more of a polyI:C adjuvant, a polyICLC adjuvant, a CpG adjuvant, a STING agonist (a c-diAMP adjuvant, a c-di-GMP adjuvant, or a c-di-CMP adjuvant), an ISCOMATRIX® adjuvant, a
PCEP adjuvant, and a Rig-I-ligand adjuvant. In certain embodiments, the adjuvant is a polyI:C adjuvant, a CpG adjuvant, a STING agonist, or a PCEP adjuvant. In certain embodiments, the adjuvant is not alum.
As used herein, an “immune stimulator” is an agent that stimulâtes an immune response that may or may not be administered independently of an antigen. Immune stimulators include, but are 20 not limited to, pegylated interferon alfa 2a (PEG-IFN-alpha-2a), interferon alfa-2b, PEG-IFN-alpha2b, interferon lambda a recombinant human interleukin-7, and a Toll-like receptor 3,7, 8 or 9 (TLR3, TLR7, TLR8, TLR9) agonist, a viral entry inhibitor (e.g., Myrcludex), an oligonucleotide that inhibits the sécrétion or release of HBsAg (e.g., REP 9AC), a capsid inhibitor (e.g., Bay41-4109 and NVR1221), a cccDNA inhibitor (e.g., IHVR-25). In certain embodiments, an immune stimulator can include a viral capsid, optionally an empty viral capsid, e.g., MVA capsid.
Immune stimulators can also include immune checkpoint regulators. Immune checkpoint regulators can be stimulatory or inhibitory. As used herein, immune checkpoint regulators potentiate an immune response. Immune checkpoint regulators include, but are not limited to, CTLA-4 inhibitors, such as ipilimumab, PD-1 inhibitors, such as Nivolumab, Pembrolizumab, and the BGB30 A317 antibody. PD-L1 inhibitors include atezolizumab, avelumab, and durvalumab, in addition to an affimer biotherapeutic.
As used herein, a “subject” is an animal, such as a mammal, including a primate (such as a human, a non-human primate, e.g., a monkey, and a chimpanzee), a non-primate (e.g., a mouse model or other animal model that can be infected with HBV). In an embodiment, the subject is a human, 35 such as a human being treated or assessed for a disease, disorder, or condition that would benefït from réduction in HBV gene expression or réplication. In certain embodiments, the subject has a chronic hepatitis B virus (HBV) infection. In certain embodiments, the subject has both a chronic hepatitis B virus (HBV) infection and a hepatitis D virus (HDV) infection.
As used herein, the terms “treating” or “treatment” refer to a bénéficiai or desired resuit including, but not limited to, alleviation of one or more signs or symptoms in a subject with HBV infection including, but not limited to, the presence of sérum HBV DNA or liver HBV ccc DNA, the presence of sérum or liver HBV antigen, e.g., HBsAg or HBeAg. Diagnostic criteria for HBV infection are well known in the art. Treatment can also mean prolonging survival as compared to expected survival in the absence of treatment, or lower risk of HCC development.
In certain embodiments, an HBV-associated disease is chronic hepatitis B (CHB). In certain embodiments, subjects hâve been infected with HBV for at least five years. In certain embodiments, subjects hâve been infected with HBV for at least ten years. In certain embodiments, subjects became infected with HBV at birth. Subjects having chronic hepatitis B disease are immune tolérant, hâve an active chronic infection accompanied by necroinflammatory liver disease, hâve increased hépatocyte tum-over in the absence of détectable necroinflammation, or hâve an inactive chronic infection without any evidence of active disease, and they are also asymptomatic. Subjects having chronic hepatitis B disease are HBsAg positive and hâve either high viremia (> 104 HBV-DNA copies / ml blood) or low viremia (<103 HBV-DNA copies / ml blood). Patients with chronic active hepatitis, especially during the high réplicative State, may hâve symptoms similar to those of acute hepatitis. The persistence of HBV infection in CHB subjects is the resuit of ccc HBV DNA persistence. In certain embodiments, a subject having CHB is HBeAg positive. In other embodiments, a subject having CHB is HBeAg négative.
In preferred embodiments, treatment of HBV infection results in a “functional cure” of hepatitis B. As used herein, the term “functional cure” is understood to be clearance of circulating HBsAg and is preferably accompanied by conversion to a status in which HBsAg antibodies become undetectable using a clinically relevant assay. For example, undetectable antibodies can include a signal lower than 10 mlU/ml as measured by Chemiluminescent Microparticle Immunoassay (CMIA) or any other immunoassay, and may be called anti-HBs séroconversion. Functional cure does not require clearance of ail réplicative forms of HBV (e.g., cccDNA from the liver). Anti-HBs séroconversion occurs spontaneously in about 0.2-1% of chronically infected patients per year. However, even after anti-HBs séroconversion, low level persistence of HBV is observed for décades indicating that a functional rather than a complété cure occurs. Without being bound to mechanism, it is proposed that the immune System is able to keep HBV in check. A functional cure permits discontinuation of any treatment for the HBV infection. However, it is understood that a “functional cure” for HBV infection may not be sufficient to prevent or treat diseases or conditions that resuit from HBV infection, e.g., liver fibrosis, HCC, cirrhosis.
The term “lower” in the context of the level of HBV gene expression or HBV réplication in a subject, or a disease marker or symptom, refers to a statistically signifîcant decrease in such level. The decrease can be, for example, at least 70%, 75%, 80%, 85%, 90%, 95%, or more. In monitoring of HBV infection, a loglO scale is typically used to describe the level of antigenemia (e.g., HBsAg level in sérum) or viremia (HBV DNA level in sérum). It is understood that a 1 loglO decrease is a
90% decrease (10% remaining), a 2 loglO decrease is a 99% decrease (1% remaining), etc. In certain embodiments, a disease marker is lowered to below the level of détection.
In certain embodiments, the expression of a disease marker is normalized, i.e., decreased to a level accepted as within the range of normal for an individual without such disorder, e.g., the level of a disease marker, such as, ALT or AST, is decreased to a level accepted as within the range of normal for an individual without such disorder. When the disease associated level is elevated from the normal level, the change is calculated from the upper level of normal (ULN). When the disease associated level is decreased from the normal level, the change is calculated from the lower level of normal (LLN). The lowering is the percent différence in the change between the subject value and the normal value. For example, a normal AST level can be reported as 10 to 40 units per liter. If, prior to treatment, a subject has an AST level of 200 units per liter (i.e., 5 times the ULN, 160 units per liter above the upper level of normal) and, after treatment, the subject has an AST level of 120 units per liter (i.e., 3 times the ULN, 80 units per liter above the upper level of normal ), the elevated AST would be lowered towards normal by 50% (80/160).
The term “inhibiting,” as used herein, is used interchangeably with “reducing,” “silencing,” “downregulating”, “suppressing”, and other similar terms, and includes any level of inhibition. Preferably inhibiting includes a statistically significant or clinically significant inhibition.
The phrase “inhibiting expression of an HBV gene” is intended to refer to knockdown of any HBV transcript (e.g., 3.5 kb, 2.4 kb, 2.1 kb, or 0.7 kb transcript) encoding one or more HBV viral proteins (such as, e.g., preSl/2-S, preS, S, P, X, preC, and C), as well as variants or mutants of an HBV gene.
“Inhibiting expression of an HBV gene” includes any significant level of inhibition of an HBV gene or transcript, e.g., at least partial suppression of the expression of an HBV gene S, P, X, or C, or any combination thereof, e.g., S, P, and C. The expression of the HBV gene may be assessed based on the level, or the change in the level, of any variable associated with HBV gene expression, e.g., an HBV mRNA level, an HBV protein level, and/or an HBV cccDNA level. This level may be assessed in an individual cell or in a group of cells, including, for example, a sample derived from a subject, e.g., levels may be monitored in sérum.
In some embodiments of the methods of the invention, expression of an HBV gene is inhibited by at least 70%, 75%, 80%, 85%, 90%, 95%, or to below the level of détection of the assay. In preferred embodiments, the inhibition of expression of an HBV gene results in a clinically relevant inhibition of the level of gene expression, e.g., sufficiently inhibited to permit an effective immune response to a vaccine against an HBV protein.
Inhibition of the expression of an HBV gene may be manifested by a réduction of the amount of RNA expressed by a first cell or group of cells (such cells may be présent, for example, in a sample derived from a subject) in which an HBV gene is transcribed and which has or hâve been treated (e.g., by contacting the cell or cells with an RNAi agent of the invention, or by administering an RNAi agent of the invention to a subject in which the cells are or were présent) such that the expression of
an HBV gene is inhibited, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has not or hâve not been so treated (control cell(s)). In preferred embodiments, the inhibition is assessed by the rtPCR method provided in Example 2 of PCT Publication No. WO 2016/077321 (the entire contents of which are incorporated herein by reference), with in vitro assays being performed in an appropriately matched cell line with the duplex at a 10 nM concentration, and expressing the level of mRNA in treated cells as a percentage of the level of mRNA in control cells, using the following formula:
(RNA incontrol cdls)—(RNA in treated cdls) e 100% RNA in control cdls ‘
Alternatively, inhibition of the expression of an HBV gene may be assessed in terms of a réduction of a parameter that is functionally linked to HBV gene expression, e.g., as described herein. HBV gene silencing may be determined in any cell expressing an HBV gene, either constitutively or by genomic engineering, and by any assay known in the art.
Inhibition of the expression of an HBV protein may be manifested by a réduction in the level of an HBV protein that is expressed by a cell or group of cells (e.g., the level of protein expressed in a sample derived from a subject). As explained above, for the assessment of mRNA suppression, the inhibition of protein expression levels in a treated cell or group of cells may similarly be expressed as a percentage of the level of protein in a control cell or group of cells or in sérum.
A control cell or group of cells that may be used to assess the inhibition of the expression of an HBV gene includes a cell or group of cells that has not yet been contacted with an RNAi agent of the invention. For example, the control cell or group of cells may be derived from an individual subject (e.g., a human or animal subject) prior to treatment of the subject with an RNAi agent. In alternative embodiments, the level may be compared to an appropriate control sample, e.g., a known population control sample.
The level of HBV RNA that is expressed by a cell or group of cells, or the level of circulating HBV RNA, may be determined using any method known in the art for assessing mRNA expression, preferably using the rtPCR method provided in Example 2 of PCT Publication No. WO 2016/077321,or Example 1 provided herein. In one embodiment, the level of expression of an HBV gene (e.g., total HBV RNA, an HBV transcript, e.g., HBV 3.5 kb transcript) in a sample is determined by detecting a transcribed polynucleotide, or portion thereof, e.g., RNA of the HBV gene. RNA may be extracted from cells using RNA extraction techniques including, for example, using acid phenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis), RNeasy RNA préparation kits (Qiagen®) or PAXgene (PreAnalytix, Switzerland). Typical assay formats utilizing ribonucleic acid hybridization include nuclear run-on assays, RT-PCR, RNase protection assays (Melton et al., Nue. Acids Res. 12:7035), northem blotting, in situ hybridization, and microarray analysis. Circulating HBV mRNA may be detected using methods the described in PCT Publication No. WO 2012/177906, the entire contents of which are hereby incorporated herein by reference.
In one embodiment, the level of expression of an HBV gene is determined using a nucleic acid probe. The term “probe”, as used herein, refers to any molécule that is capable of selectively binding to a spécifie HBV gene. Probes can be synthesized by one of skill in the art, or derived from appropriate biological préparations. Probes may be specifically designed to be labeled. Examples of molécules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molécules.
Isolated RNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or northem analyses, polymerase chain reaction (PCR) analyses, and probe arrays. One method for the détermination of mRNA levels involves contacting the isolated mRNA with a nucleic acid molécule (probe) that can hybridize to an HBV mRNA. In one embodiment, the mRNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose. In an alternative embodiment, the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix® gene chip array. A skilled artisan can readily adapt known mRNA détection methods for use in determining the level of an HBV mRNA.
An alternative method for determining the level of expression of an HBV gene in a sample involves the process of nucleic acid amplification or reverse transcriptase (to préparé cDNA) of, for example mRNA in the sample, e.g., by RT-PCR (the experimental embodiment set forth in Mullis,
1987, US Patent No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA
88:189-193), self sustained sequence réplication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification System (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), rolling circle réplication (Lizardi et al., US Patent No. 5,854,033) or any other nucleic acid amplification method, followed by the détection of the amplified molécules using techniques well known to those of skill in the art. These détection schemes are especially useful for the détection of nucleic acid molécules if such molécules are présent in very low numbers. In particular aspects of the invention, the level of expression of an HBV gene is determined by quantitative fluorogenic RT-PCR (i.e., the TaqMan™ System), e.g., using the method provided herein.
The expression levels of an HBV RNA may be monitored using a membrane blot (such as used in hybridization analysis such as northem, Southern, dot, and the like), or microwells, sample tubes, gels, beads, or fibers (or any solid support comprising bound nucleic acids). See U.S. Patent Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195, and 5,445,934, the entire contents of each of which are incorporated herein by reference. The détermination of HBV expression level may also comprise using nucleic acid probes in solution.
In preferred embodiments, the level of RNA expression is assessed using real time PCR (qPCR). The use of these methods is described and exemplified in the Examples presented herein.
The level of HBV protein expression may be determined using any method known in the art for the measurement of protein levels. Such methods include, for example, electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdifïusion chromatography, fluid or gel precipiting reactions, absorption spectroscopy, a colorimétrie assays, spectrophotometric assays, flow cytometry, immunodiffusion (single or double), immunoelectrophoresis, western blotting, radioimmunoassay (RIA), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, electrochemiluminescence assays, and the like.
In some embodiments, the efficacy of the methods of the invention can be monitored by detecting or monitoring a réduction in a symptom of an HBV infection. Symptoms may be assessed 10 using any method known in the art.
As used herein, the term Hepatitis B virus-associated disease” or “HBV-associated disease,” is a disease or disorder that is caused by, or associated with HBV infection or réplication. The term HBV-associated disease” includes a disease, disorder, or condition that would benefit from réduction in HBV gene expression or réplication. Non-limiting examples of HBV-associated diseases include, 15 for example, hepatitis D virus infection,; hepatitis delta; chronic hepatitis B; liver fîbrosis; end-stage liver disease; cryoglobulinemia; hepatocellular carcinoma.
The term “sample,” as used herein, includes a collection of similar fluids, cells, or tissues isolated from a subject or prepared therefrom, as well as fluids, cells, or tissues présent within a subject. Examples of biological fluids include blood, sérum, plasma, immune cells, lymph, urine, 20 saliva, and the like. Tissue samples may include samples from tissues, organs, or localized régions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hépatocytes, résident liver immune cells). In preferred embodiments, a “sample derived from a subject” refers to blood drawn 25 from the subject or plasma, sérum, or selected cell pools derived therefrom (e.g., populations of immune cells). In further embodiments, a “sample derived from a subject” refers to liver tissue (or subcomponents thereof) obtained from the subject.
As used herein, “coding sequence is understood to refer to a DNA sequence that encodes for a spécifie amino acid sequence. In certain embodiments, the DNA sequence can be reverse transcribed from an RNA sequence. In certain embodiments, an iRNA, e.g., an shRNA, targets a coding sequence. .
The terms, suitable regulatory sequences, and the like, are used herein is to refer to nucléotide sequences located upstream (5' non-coding sequences), within, or downstream (3' noncoding sequences) of a coding sequence, and which influence the transcription, RNA processing or 35 stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation récognition sequences.
Promoter as used herein refers to a DNA sequence capable of controlling the expression of a coding sequence or fimctional RNA. In general, a coding sequence is located 3' to a promoter c/ sequence. Promoters may be denved m their entirety from a native gene, or be composed of different éléments derived from different promoters found in nature, or even comprise synthetic DNA segments. A promoter may be selected to promote expression of a coding sequence in a particular cell type or at different stages of development, or in response to different environmental conditions. In certain embodiments, the promoter is a promoter that is active in liver, e.g., a liver-specific promoter. Many promoter sequences are known in the art and sélection of an appropriate promoter sequence for a spécifie context is within the ability of those of skill in the art.
The term operably linked refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter).
The term expression as used herein refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA, or an RNAi agent (e.g., an shRNA) derived from the nucleic acid fragment of the subject technology. Over-expression refers to the production of a gene product in transgenic or recombinant organisms that exceeds levels of production in normal or non-transformed organisms.
“Expression vector” or “expression construct,” as used herein, refers to a nucleic acid in which a coding sequence is operably linked to a promoter sequence to permit expression of the coding sequence under the control of the promoter. Expression vectors include, but are not limited to, viral vectors or plasmid vectors. Methods for delivery of expression vectors into cells are known in the art.
II. Treatment Methods of the Invention
The présent invention provides treatment regimens and methods for the sequential use of an agent to reduce the expression of an HBV gene, e.g., iRNA agents which effect the RNA-induced silencing complex (RlSC)-mediated cleavage of one or more HBV transcripts, and hepatitis B vaccines to stimulate an immune response against one or more HBV proteins in the treatment of HBV infection. The treatment regimens and methods preferably provide a functional cure of HBV within a defined period of time.
The treatment regimens and methods provided herein include the ordered administration of therapeutic agents to provide treatment, and preferably a functional cure, for HBV infection. The agents used in the methods are known in the art. However, the agents alone fail to consistently and durably decrease HBV disease burden, e.g., reducing HBsAg levels to below 2 loglO, preferably 1 loglO lU/ml or to below the level of détection, in most subjects. Significantly reducing HBV disease burden, e.g., reducing HBsAg levels to below 2 loglO, preferably 1 loglO lU/ml or to below the level of détection, will provide the opportunity of discontinuation of administration of therapeutic agents and provide a functional cure for HBV in a substantial number of subjects. Without being bound by mechanism, it is proposed that the treatment regimens and methods provided herein, including administration of an iRNA agent targeted to HBV, substantially reduces HBV antigens and nucleic
acid for a sufficient magnitude and duration in a subject to allow an effective immune response induced by administration of multiple doses of a therapeutic vaccine. The regimens and methods, provided herein, consistently provide a substantial réduction of disease burden and a functional cure in a significant number of subjects, preferably at least 30%, 40%, 50%, 60%, or 70% of subjects.
A transgenic mouse model of HBV infection, HBV1.3 xfs was used to assess the combination therapy provided herein. Primary studies demonstrated the efficacy of two different chemically modified GalNAc- iRNA agents targeted to HBV (AD-66816 and AD-66810) to inhibit the level of HBsAg and HBeAg proteins, and HBV DNA in sérum for at least 21 days with a single subcutaneous dose at 3 mg/kg or 9 mg/kg, with similar efficacy. No significant knockdown was observed with a non-HBV iRNA control (see Figure 2). Based on this resuit, the lower dose of 3 mg/kg was selected for combination therapy studies.
In the first combination therapy trial (see Figure 3), mice were pretreated with one of six treatment regimens (n= 6 per group):
(1) No pretreatment;
(2) Entecavir at 1 pg/ml in water throughout the course of the study beginning on the first day ofWeekO;
(3) A 3 mg/kg dose on the first day of Weeks 0,4,8, and 12 of the control iRNA agent.
(4) A single dose on the first day of Week 0 with an expression vector encoding an shRNA targeted to HBV (HBV-shRNA) (Michler et al., 2016); or (5-6) A 3 mg/kg dose on the first day of Weeks 0,4, 8, and 12 of AD-66816 or AD-66810 (generically, HBV-siRNA).
On the first day of Weeks 12 and 14, a mixture of recombinantly expressed yeast HBsAg (15 pg) and E. coli expressed HBcAg (15 pg) adjuvanted with 31.9 pg synthetic phosphorothioated CpGODN 1668 (CpG) and 25 pgpoly[di(sodiumcarboxylatoethyl-phenoxy)phosphazene] (PCEP) was subcutaneously administered to ail mice as a protein prime vaccination (Backes, 2016).
On the first day of week 16, a mixture of modified vaccinia virus Ankara expressing HBsAg or HBcAg (5 x 107 particles of each virus) was subcutaneously administered to ail mice as a boost vaccination (Backes, 2016).
Blood samples were obtained on the first days of Week 0,2,4, 8,12,16, and 17 and were assayed for levels of HBsAg, HBeAg, and HBV DNA. Results observed for HBsAg and HBeAg levels mice in groups 1,2, and 3 (mock, Entecavir, control iRNA agent) were similar (Figure 4A and 4B). The HBV-shRNA or HBV-siRNAs alone caused a significant decrease in HBsAg, HBeAg, and HBV DNA in sérum. The three dose prime-boost vaccination scheme resulted in a further decrease in HBsAg in ail groups, and reduced the level of HBsAg in at least some animais in the HBV-shRNA and HBV-siRNA groups to below the level of détection. However, vaccine treatment did not decrease
HBeAg levels in any of the groups. HBV DNA levels were decreased to about the lower limit of quantitation with Entecavir alone so no effect of the three dose prime-boost vaccine could be detected (Figure 4C). Mock treatment and treatment with the HBV-shRNA, the HBV-siRNAs, and control siRNA ail decreased HBV DNA levels, and the level of HBV-DNA was further decreased by the pnme-boost vaccine in ail groups. These data demonstrate that RNAi is superior to nucleot(s)ide analog therapy in reducing viral antigens. Also, the combination of RNAi and subséquent vaccination hâve a greater effect on HBsAg and HBV DNA levels than either agent alone.
On the final day of the experiment (the first day of week 17), mice were sacrificed and their livers were harvested. Intrahepatic CD8+ T cell responses were assessed for response to HBsAg, HBcAg, and the MVA virus particle using the method provided in Backes, 2016. Mice treated with the HBV-shRNA or the HBV-siRNAs were able to generate a CD8+ immune response against the HBsAg and HBcAg (Figure 5A and 5B). No significant immune response against the HBV antigens was observed in the mock, Entecavir, or control siRNA groups. However, a similar immune response against the MVA virus was observed in ail animais independent of pretreatment or viral antigen levels (Figure 5C) showing that vaccination had worked equally well in ail animais, demonstrating the presence of a competent immune system. The data shown in Figure 5A-C were reanalyzed to accomodated for an insufficient exclusion of dead immune cells during the first analysis. The data obtained from the second analysis (shown in Figure 5 D-F) again shows that only the mice pretreated with the HBV-shRNA or the HBV-siRNAs were able to generate HBV-specific CD8+ T cell responses after therapeutic vaccination, but that MVA-specific responses were not influenced by the pretreatment. The reduced variances in the second analysis are attributed to the more rigorous exclussion of dead cells. These data demonstrate that RNAi treatment, in contrast to the current standard of care treatment with a nucleoside analog, can restore HBV-specific T cell immunity and enable the induction of HBV-specific CD8 T cell responses after therapeutic vaccination.
Sérum was also assessed for antibody immune response to HBV antigens. Although the vaccine was able to induce a T-cell immune response only in animais which had received HBVsiRNA or HBV-shRNA pretreatment, antibody responses against HBsAg and HBcAg were similar across ail groups regardless of pretreatment at the time points evaluated until week 17. No HBeAg antibody responses could be detected. These data demonstrate that high HBV antigen loads preferentially inhibit HBV-specific T cell, not B cell responses.
Livers were also assessed for the presence of HBV transcripts by RT-qPCR and normalized to the liver GAPDH transcript. Mice treated with the HBV-shRNA or the HBV-siRNAs demonstrated a significant decrease in HBV transcript levels (Figure 6A and 6B). No significant différence was observed between the mock and Entecavir or control siRNA groups. Liver sections were analysed by immunohistochemical stainings for expression of core antigen to assess the antiviral effect in the liver (Figure 6C). In animais that were not pretreated before vaccination, there were, on average, 83 hépatocytes per mm2 with cytoplasmic expression of HBc. This number was not significantly changed in animais that were pretreated with Entecavir or the control siRNA. However, the number of cytoplamic HBcAg positive cells was significantly reduced in AAV-shRNA or HBV siRNA pretreated animais. These data demonstrate that a combinatorial RNAi/vaccination therapy suppresses not only antigens in the sérum, but also viral antigen expression in the liver.
Having demonstrated that suppression of expression of HBV antigens using shRNA or siRNA is effective at potentiating an immune response to an HBV vaccine regimen, a study was designed to détermine if the duration of HBV antigen suppression had an effect on the potentiation an HBV immune response. Using the HBV 1.3xfs mouse model, mice were treated for eight, six, or three weeks with HBV-siRNA AD-66816, or the control siRNA for 8 weeks, subcutaneously administered at 3 mg/kg/dose, followed by administration of the prime-boost vaccine regimen as set forth above, except 10 pg c-di-AMP was used as an adjuvant rather than PCEP + CPG (n= 6 per 8 and 3 group, n = 6 for 6 week group) (see Figure 7).
A significant decrease in the levels of each of HBsAg, HBeAg, and HBV DNA was observed 10 after the first administration of AD-66816 (Figures 8A-8C). A further significant decrease in HBsAg was observed after treatment with the vaccine boost with the greatest decrease observed in the 8 week pretreatment group to below the level of détection of the assay, representing a greater than 5 loglO decrease in HBsAg level in ail treated animais. Immunization caused only slight further réductions (<0.5 loglO) of HBV DNA and no further réduction in HBeAg levels. These data demonstrate that 15 efficacy of therapeutic vaccination correlates with duration of antigen suppression before start of vaccination. Reconstitution of HBV-specific CD8 T cell responses takes several weeks, with a 6 or preferably 8 week pretreatment resulting in more HBsAg knockdown than a 3 week pretreatment.
Similarly, T-cell responses against HBsAg and HBeAg in liver corresponded with the duration of HBV antigen knockdown, with longer duration of HBV antigen suppression resulting in 20 greater T-cell responses (Figure 9A-9C). Similar responses to MVA virus antigens were observed across ail groups independent of pretreatment (Figure 9D). Antibody responses were similar across ail groups.
Livers were also assessed for the presence of HBV transcripts by RT-qPCR and normalized to the liver GAPDH transcript. Longer pretreatment durations trended to higher levels of HBV RNA knockdown (Figure 1 OA and 10B).
Liver sections were also analysed by immunohistochemical staining for cytoplasmic expression of HBeAg to assess the antiviral effect of the treatment in the liver (Figure 10C). In animais pretreated with the control siRNA before vaccination, there were, on average, 172 hépatocytes per mm2 which showed cytoplasmic expression of HBc. With longer duration of HBV 30 suppression before vaccination, there was a graduai decrease of cytoplasmic HBeAg positive hépatocytes with an average of only 12 cytoplasmic HBcAgpositive hépatocytes per mm2 in the 8 week pretreatment group. These data demonstrate that the increasing HBV-specific CD8+ T cell response observed with longer antigen suppression before vaccination led to decreased HBV antigen expression in the liver. To assess the durability of response, blood samples were collected from mice 35 (n = 6) pretreated with the AD-66816 HBV-siRNA for six weeks at 2 and 3 weeks after administration of the boost vaccination. In three of the six mice, HBsAg levels continued to dropped to below the level of détection of the assay (Figure 11A and 1 IB). Specifically, the three animais which had the highest HBsAg and HBeAg levels at start of vaccination (2,4, and 5) did show a
décliné of antigen titers after vaccination, but rebounded with antigen titers towards the end of the expenment. In contrast, the three animais with the lowest antigen titers at start of vaccination (1,3, and 6) showed a further décliné of HBsAg to below the détection limit. These data demonstrate that a functional cure is possible using the treatment regimens provided herein. These data also suggest that the antigen levels at start of vaccination can affect the response to therapeutic vaccination. Finally, without being bound by mechanism, these data suggest that the décliné of antigen levels after therapeutic vaccination is mediated, at least in part, by CD8+ T cells. These data demonstrate that knockdown of circulating HBV antigens (e.g., HBsAg, HBcAg), but not inhibition of HBV DNA réplication alone, potentiates immune response to HBV therapeutic vaccine, e.g., a prime boost therapeutic vaccination regimen. That is, an immune response can be potentiated by pretreatment with an siRNA, but not with nucleot(s)ide inhibitors alone as the immune response is a CD8+ T-cell based immune response.
The magnitude and duration of knockdown required dépends on, for example, the level of disease burden in the subject. The higher the level of circulating antigen, the greater the magnitude and duration of HBV antigen knockdown required to potentiate an immune response. Knockdown of HBsAg in sérum should be at least 0.5 log 10 (lU/ml), preferably llog 10 (HJ/ml), 1.5 log 10 (lU/ml), 2 log 10 (lU/ml), or more from the level in the subject prior to treatment with the therapeutic vaccine. In certain embodiments, the level of sérum HBsAg is no more than 2.5 log 10 (lU/ml), 2 log 10 (lU/ml), 1.5 log 10 (lU/ml) prior to vaccine administration.
Further, as demonstrated herein, a longer duration of HBV antigen knockdown trended towards a more robust immune response. Therefore, knockdown of sérum HBsAg to a sufïiciently low level for a duration of at least four weeks, six weeks, or eight weeks is preferred prior to administration of the vaccine.
A second sériés of experiments were designed to study the combination siRNA/vaccination treatment regimen in a mouse model of aquired HBV infection using an adeno-associated virus infection system. For these studies, wildtype C57/B16 mice (9 weeks of âge) were injected i.v. with 2x10'° genome équivalents of Adeno-Associated-Virus Serotype 8 (AAV8) carrying a 1.2-fold overlength HBV genome of génotype D (AAV-HBV1.2) (see, e.g., Yang, et al. (2014) Cell and Mol Immunol 11:71). Starting 4 weeks after AAV-transduction (on day -28), animais were treated with three doses of either a control siRNA, or HBV siRNA (HBV AD-66816 or AD-66810) on days 0,29, and 57, and subsequently half of the animais in each group were treated with a vaccine regimen consisting of prime protein vaccination with HBsAg, HbcAg, and 10 pg c-di-AMP at days 57 and 70, and boosted with MVA-HBs and MVA-HBc at day 84. The treatment regimen is shown in Figure 12.
Following AAV-HBV1.2 transduction, HBsAg and HBeAg values rose to levels comparable to the levels seen in HBV transgenic mice (HBVxfs) (see, e.g., Figures 13A and 13B). Mice treated with the HBV siRNAs showed mean réductions of HBsAg levels of about 2 logio scales and of HBeAg levels greater than 1 logio scale such that HBsAg and HBeAg levels dropped to less than about 500 lU/per ml, whereas the control siRNA had no effect on antigen levels. Animais treated with
one of the HBV siRNAs that did not receive the vaccine regimen showed slowly rebounding antigen levels after the last application of the siRNA. Antigenemia retumed to baseline levels after 18 weeks. The combination treatment with the HBV-siRNA and vaccine regimen resulted in a durable response with a decrease in HBsAg and HBeAg to below the limit of détection through the duration of the experiment. A decrease in HBsAg and HBeAg levels was observed prior to the administration of the MVA boost, suggesting that the protein vaccination may be sufficient to affect a cure. Both sérum and liver HBV DNA and RNA were significantly decreased after combination treatment with the HBVsiRNA and vaccine regimen (Figures 13D-13H). This demonstrates, that RNAi-mediated suppression can strongly reduce antigen expression, but that treatment with the vaccine regimen extends the durability of response.
The vaccine regimen alone in animais that received the control siRNA produced a transient décliné of antigen levels which rebounded towards the end of the experiment. In contrast, ail animais that received an HBV-siRNA and vaccination, HBsAg and HBeAg levels decreaased to below the détection limit after start of vaccination. Antigen levels remained largely undetectable at ail through the last time point measured at least 22 weeks after the last siRNA application (Figures 13A and 13B). The durable loss of antigenemia in HBV siRNA pretreated animais, in contrast to the antigen rebound in control siRNA pretreated animais, further demonstrates that immune control was only achieved in animais which had lowered antigen titers before vaccination.
Coinciding with the loss of antigenemia, animais treated with HBV siRNA plus the vaccine regimen developed high titers of anti-HBs antibodies and resulted in anti-HBs and anti-HBe séroconversion in ail vaccinated animais (Figure 14). siRNA-pretreated animais developed 10-fold higher and more constant anti-HBs titers and were able to completely and persistently clear sérum HBsAg and HBeAg. Interestingly, 3/12 mice vaccinated after HBV siRNA treatment showed a transient drop in anti-HBe levels between week 15 and 22 resulting in a low-level relapse of HBeAg (Figure 13C) that was again controlled. Although anti-HBs antibodies could also be measured in animais that received the control siRNA plus the vaccine regimen, the levels were lower. Further, only animais that received HBV siRNA plus the vaccine regimen developed anti-HBe antibodies. Taken together, functional cure was not achieved by the siRNA treatement regimen or the therapeutic vaccination regimen alone. However, the loss of antigenemia, as well as development of anti-HBs and anti-HBe antibodies, demonstrates that the combination HBV siRNA plus vaccine regimen can achieve a functional cure.
Throughout the experiment, ALT and body weight of the animais were monitored. The loss of antigenemia concided with slight increases of ALT activity seen in treatment groups which had received HBV siRNA in conjunction with the vaccination regimen (Figure 15A). These groups showed significant but mild increases (both p>0.05 or smaller by repeated measure two-way ANOVA; only comparing time points after start of vaccination) as compared to ail other treatment groups that did not receive the combination HBVsiRNA-vaccine regimen. Without being bound by
mechanism, it is suggested that the CD8+ T cells induced by the combinatorial HBV siRNA-vaccine regimen killed HBV-expressing hépatocytes resulting in elevated ALT.
The body weight of the animais was measured throughout the experiment to assess tolerability of the treatments. There was steady increases throughout the experiment independent of siRNA treatment. Animais that were vaccinated showed a slight and transient decrease (approximately 5%) of body weight after vaccination, but rebounded to normal levels within nine days, and subsequently gained weight comparable to the control groups (Figure 15B). Taken together, both, ALT activity and body weight data demonstrate that ail examined treatments, including siRNA only, vaccine only, as well as the combinatorial siRNA/vaccine regimen are well tolerated.
The number and timing of doses of siRNA to knockdown HBsAg level in sérum dépends, for example, on the spécifie agent used. Due to the duration and potency of the exemplary GalNAc siRNAs used in the methods herein and provided, for example, in Appendix A and in PCT Publication No. WO 2016/077321 (the entire contents of which are incorporated herein by reference), a single dose of siRNA may be sufficient to provide the level and duration of knockdown required prior to administration of the therapeutic vaccine. As shown in Figure 4, a single dose of an AAV vector encoded shRNA was sufficient to provide durable knockdown of HBV antigens and HBV DNA. Those of skill in the art are able to monitor HBV disease status, e.g., by measuring HBsAg levels in blood, to détermine the timing and level of siRNA and vaccine administration appropriate for a spécifie subject.
A number of therapeutic HBV vaccines are known in the art and discussed herein. In preferred embodiments, a prime-boost vaccination protocol, such as the protocol that is used herein, is preferred. However, the HBV antigen knockdown method provided herein can be used in combination with other therapeutic HBV vaccines known in the art, including those found to be insufficient when administered alone. Vaccinations include at least two doses of an antigen in protein or nucleic acid form. In certain embodiments, the vaccination includes three doses of a protein-based vaccine. In preferred embodiments, the methods include heterologous vaccine administration, i.e., at least one protein-based vaccine dose and at least one nucleic-acid based vaccine dose. Exemplary embodiments of vaccines and dosing regimens are provided, for example, in PCT Publication No. WO 2017/121791, the entire contents of which are incorporated herein by reference.
The methods provided herein include the use of a nucleic acid-based vaccine comprising an expression vector construct encoding an HBcAg or an HBsAg, wherein the construct encodes a protein that shares an epitope with the protein-based vaccine. Therefore, it is clearly understood that neither the nucleic acid-based vaccine nor the protein-based vaccine are required to provide the full length protein. The nucleic acid-based vaccine and the protein-based vaccine are required to provide at least one shared epitope that is présent in HBcAg or HBsAg, and does not require that the full length protein be provided. As noted above, epitopes may be relatively short, MHC class I molécules that are typically peptides about 8 to 11 amino acids in length, whereas MHC class Π molécules présent longer peptides about 13 to 17 amino acids in length, with conformational epitopes being
longer. However, it is understood that the use of protein antigens and coding sequences for protein antigens that encode multiple epitopes is preferred. Further, it is understood that the antigens présent in the protein-based vaccine and encoded by the nucleic-acid based vaccine may or may not be identical. It is also obvions that antigens should also be selected for their immunogenicity. Such antigens are well known in the art.
In certain embodiments, the order of administration of the protein-based vaccine and the nucleic acid-based vaccine are reversed as compared to the order exemplifïed in the methods provided herein. That is, the nucleic acid-based vaccine is administered first and the protein-based vaccine is administered second. In certain embodiments, a total of three doses of vaccine are administered, two doses of the nucleic acid-based vaccine followed by a single dose of the protein-based vaccine. In alternative embodiments, a single dose of the nucleic acid-based vaccine is followed by two doses of a protein based vaccine. In other embodiments, one dose of each vaccine is administered.
In preferred embodiments, the prime-boost vaccination method includes the use of an adjuvant with protein antigens. Appropriate adjuvants for use in the methods promote a cell-based response to the antigens. Adjuvants preferably provide a balanced Thl/Th2 response.
The siRNA + vaccine methods provided herein can be used in combination with administration of nucleot(s)ide inhibitors which are the standard of care for treatment of HBV. In certain embodiments, subjects are treated with nucleot(s)ide inhibitors prior to treatment with the siRNA + vaccine treatment regimen. In certain embodiments, subjects are treated throughout the siRNA + vaccine treatment regimen with nucleot(s)ide inhibitors. In certain embodiments, the nucleot(s)ide inhibitor is dosed to reduce pre-existing inflammation associated with HBV infection prior to administration of the nucleic acid therapeutic targeted to HBV (e.g., siRNA, shRNA, antisense oligonucleotide).
In certain embodiments, subjects may be pretreated, or concurrently treated, with other agents used for the treatment of HBV. Such agents include, but are not limited to an immune stimulator (e.g., pegylated interferon alfa 2a (PEG-IFN-a2a), Interferon alfa-2b, a recombinant human interleukin-7, and aToll-like receptor 7 (TLR7) agonist), a viral entry inhibitor (e.g., Myrcludex), an oligonucleotide that inhibits the sécrétion or release of HbsAg (e.g., REP 9AC), a capsid inhibitor (e.g., Bay41-4109 and NVR-1221), a cccDNA inhibitor (e.g., IHVR-25), a Rig-I ligand, or an immune checkpoint regulator. In certain embodiments, the immune stimulator is a Rig-I ligand or an immune checkpoint regulator. A functional cure includes a sustained period of at least 3 months, preferably 6 months of HBsAg below 50 lU/ml, or a détectable antibody response to HBsAg. In preferred embodiments, a functional cure includes both a sustained period of at least 3 months, preferably 6 months of HBsAg below 50 lU/ml and a détectable antibody response to HBsAg.
A. RNAi Agents For Use in the Methods of the Invention
The présent invention includes the use of iRNAs, which inhibit the expression of at least one HBV transcript, and preferably three or four HBV transcripts (open reading fiâmes, sometimes referred to herein as genes). Due to the highly condensed structure of the HBV genome, it is possible to design smgle iRNAs that will inhibit the expression of three or four HBV transcripts (see Figure 1). For the sake of simplicity, the text herein refers to “an HBV transcript” or “the HBV transcript.” It is understood that preferred embodiments include inhibition of more than one HBV transcript (or open reading frame), preferably at least three HBV transcripts (or open reading frames). Further, it is understood that there are eight HBV génotypes, and two proposed additional génotypes, that may further include mutations from published sequences. Therefore, certain iRNA agents may inhibit different numbers of genes based on the spécifie génotype and subject infected with HBV.
In some embodiments, the iRNA agent includes double stranded ribonucleic acid (dsRNA) molécules for inhibiting the expression or decreasing the level of an HBV transcript in a cell in a subject with an HBV infection. The dsRNA includes an antisense strand having a région of complementarity, which is complementary to at least a part of an mRNA formed in the expression of an HBV transcript. The région of complementarity is about 30 nucléotides or less in length (e.g., about 30,29,28,27,26,25,24,23,22,21,20,19, or 18 nucléotides or less in length). Upon contact with a cell expressing the HBV gene, the iRNA selectively inhibits the expression of at least one, preferably three or four HBV genes. In preferred embodiments, inhibition of expression is determined by the qPCR method in an appropriate cell line as provided in the examples. For in vitro assessment of activity, percent inhibition is determined using the methods provided in Example 2 of PCT Publication No.WO 2016/077321 at a single dose at a 10 nM duplex final concentration. For in vivo studies, the level after treatment can be compared to, for example, an appropriate historical control or a pooled population sample control to détermine the level of réduction, e.g., when a baseline value is not available for the subject. An appropriate control must be carefully selected by one of skill in the art.
A dsRNA includes two RNA strands that are complementary and hybridize to form a duplex structure under conditions in which the dsRNA will be used. One strand of a dsRNA (the antisense strand) includes a région of complementarity that is substantially complementary, and generally fully complementary, to a target sequence. The target sequence can be derived from the sequence of an mRNA formed during the expression of an HBV gene. As multiple HBV génotypes are known, iRNA agents are preferably designed to inhibit expression of HBV genes across as many génotypes as possible. It is understood that an siRNA that is perfectly complementary to one or more HBV génotypes will not be perfectly complementary to ail génotypes. The other strand (the sense strand) includes a région that is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions. As described elsewhere herein and as known in the art, the complementary sequences of a dsRNA can also be contained as selfcomplementary régions of a single nucleic acid molécule, as opposed to being on separate oligonucleotides.
Generally, the duplex structure is 15 and 30 base pairs in length, e.g., 15-29,15-28,15-27, 15-26, 15-25, 15-24, 15-23, 15-22, 15-21,15-20, 15-19, 15-18, 15-17, 18-30, 18-29, 18-28, 18-27, 18-
26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30, 19-29,19-28,19-27, 19-26,19-25, 19-24, 19-23,
19-22, 19-21,19-20, 20-30,20-29, 20-28,20-27,20-26,20-25, 20-24,20-23,20-22,20-21,21-30, 2129,21-28, 21-27, 21-26,21-25, 21-24, 21-23, or 21-22 base pairs in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the invention.
Similarly, the région of complementarity to the target sequence is 15 and 30 nucléotides in length, e.g., 15-29, 15-28,15-27,15-26,15-25, 15-24, 15-23,15-22, 15-21, 15-20,15-19,15-18, 1517,18-30, 18-29, 18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22,18-21,18-20, 19-30, 19-29, 19-28, 19-27, 19-26,19-25, 19-24, 19-23, 19-22, 19-21, 19-20,20-30, 20-29, 20-28, 20-27,20-26, 20-25, 2024,20-23, 20-22,20-21,21-30, 21-29,21-28,21-27,21-26,21-25,21-24, 21-23, or 21-22 nucléotides in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the invention.
In some embodiments, the dsRNA is about 15 to 20 nucléotides in length, or about 25 to 30 nucléotides in length. In general, the dsRNA is long enough to serve as a substrate for the Dicer enzyme. For example, it is well-known in the art that dsRNAs longer than about 21-23 nucléotides in length may serve as substrates for Dicer. As the ordinarily skilled person will also recognize, the région of an RNA targeted for cleavage will most often be part of a larger RNA molécule, often an mRNA molécule. Where relevant, a “part” of an mRNA target is a contiguous sequence of an mRNA target of sufficient length to allow it to be a substrate for RNAi-directed cleavage (i.e., cleavage through a RISC pathway).
One of skill in the art will also recognize that the duplex région is a primary functional portion of a dsRNA, e.g., a duplex région of about 9 to 36 base pairs, e.g., about 10-36, 11-36, 12-36, 13-36, 14-36, 15-36, 9-35, 10-35, 11-35, 12-35, 13-35, 14-35, 15-35, 9-34, 10-34, 11-34, 12-34, 1334, 14-34, 15-34, 9-33, 10-33, 11-33, 12-33, 13-33, 14-33, 15-33, 9-32, 10-32, 11-32, 12-32, 13-32, 14-32, 15-32,9-31, 10-31,11-31,12-31, 13-32, 14-31, 15-31, 15-30, 15-29, 15-28, 15-27, 15-26, 1525, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17,18-30, 18-29, 18-28,18-27, 18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20,19-30, 19-29, 19-28, 19-27, 19-26,19-25, 19-24, 19-23, 19-22, 1921,19-20, 20-30,20-29,20-28,20-27,20-26,20-25, 20-24,20-23,20-22, 20-21, 21-30, 21-29,21-28, 21-27, 21-26,21-25,21-24,21-23, or 21-22 base pairs. Thus, in one embodiment, to the extent that it becomes processed to a functional duplex, of e.g., 15-30 base pairs, that targets a desired RNA for cleavage, an RNA molécule or complex of RNA molécules having a duplex région greater than 30 base pairs is a dsRNA. Thus, an ordinarily skilled artisan will recognize that in one embodiment, à miRNA is a dsRNA. In another embodiment, a dsRNA is not a naturally occurring miRNA. In another embodiment, an iRNA agent useful to target HBV gene expression is not generated in the target cell by cleavage of a larger dsRNA.
The duplex région may be of any length that permits spécifie dégradation of a desired target RNA through a RISC pathway, and may range from about 9 to 36 base pairs in length, e.g., about 1530 base pairs in length, for example, about 9, 10, 11,12,13, 14, 15, 16, 17, 18, 19,20, 21,22,23, 24, 25,26,27,28,29,30,31,32,33, 34,35, or 36 base pairs in length, such as about 15-30, 15-29,15-28,
15-27, 15-26,15-25, 15-24, 15-23,15-22,15-21, 15-20, 15-19, 15-18, 15-17, 18-30,18-29,18-28, 1827,18-26, 18-25, 18-24,18-23, 18-22, 18-21, 18-20, 19-30,19-29,19-28, 19-27,19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20,20-30,20-29,20-28,20-27,20-26, 20-25, 20-24,20-23,20-22, 20-21, 2130,21-29,21-28, 21-27,21-26,21-25,21-24,21-23, or 21-22 base pairs in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the invention.
The two strands forming the duplex structure may be different portions of one larger RNA molécule, or they may be separate RNA molécules. Where the two strands are part of one larger molécule, and therefore are connected by an uninterrupted chain of nucléotides between the 3’-end of 10 one strand and the 5’-end of the respective other strand forming the duplex structure, the connecting
RNA chain is referred to as a “hairpin loop.” A hairpin loop can comprise at least one unpaired nucléotide. In some embodiments, the hairpin loop can comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 23 or more unpaired nucléotides.
In some embodiments, a dsRNA agent of the invention comprises a tetraloop. As used herein, tetraloop in the context of a dsRNA refers to a loop (a single stranded région) consisting of four nucléotides that forms a stable secondary structure that contributes to the stability of adjacent Watson-Crick hybridized nucléotides. Without being limited to theory, a tetraloop may stabilize an adjacent Watson-Crick base pair by stacking interactions. In addition, interactions among the four 20 nucléotides in a tetraloop include, but are not limited to, non-Watson-Crick base pairing, stacking interactions, hydrogen bonding, and contact interactions (Cheong et al., Nature 1990 Aug
16;346(6285):680-2; Heus and Pardi, Science 1991 Jul 12;253(5016): 191-4). A tetraloop confers an increase in the melting température (Tm) of an adjacent duplex that is higher than expected from a simple model loop sequence consisting of four random bases. For example, a tetraloop can confer a 25 melting température of at least 55°C in lOmM NaHPCL to a hairpin comprising a duplex of at least 2 base pairs in length. A tetraloop may contain ribonucleotides, deoxyribonucleotides, modified nucléotides, and combinations thereof. Examples of RNA tetraloops include the UNCG family of tetraloops (e.g., UUCG), the GNRA family of tetraloops (e.g., GAAA), and the CUUG tetraloop. (Woese et al., Proc Natl Acad Sci USA. 1990 Nov;87(21):8467-71 ; Antao et al., Nucleic Acids Res. 30 1991 Nov 11; 19(21):5901 -5). Examples of DNA tetraloops include the d(GNNA) family of tetraloops (e.g., d(GTTA), the d(GNRA)) family of tetraloops, the d(GNAB) family of tetraloops, the d(CNNG) family of tetraloops, the d(TNCG) family of tetraloops (e.g., d(TTCG)). (Nakano et al. Biochemistry, 41 (48), 14281 -14292,2002; Shinji et al. Nippon Kagakkai Koen Yokoshu vol.78th; no.2; page.731 (2000).)
In certain embodiments of the invention, tetraloop- and modified nucléotide- containing dsNAs are contemplated as described, e.g., as described in U.S. Patent Publication No. 2011/0288147, the entire contents of which are incorporated by reference herein. In certain such embodiments, a dsNA of the invention possesses a first strand and a second strand, where the first strand and the second strand form a duplex région of 19-25 nucléotides in length, wherein the first strand comprises a 3 région that extends beyond the first strand-second strand duplex région and comprises a tetraloop, and the dsNA comprises a discontinuity between the 3' terminus of the first strand and the 5' terminus of the second strand.
Optionally, the discontinuity is positioned at a projected Dicer cleavage site of the tetraloopcontaining double stranded nucleic acid (dsNA). It is contemplated that, as for any of the other dupexed oligonucleotides of the invention, tetraloop-containing duplexes of the invention can possess any range of modifications disclosed herein or otherwise known in the art, including, e.g., 2'-Omethyl, 2'- fluoro, inverted base, GalNAc moieties, etc. Typically, every nucléotide on both strands of the tetraloop-containing dsNA is chemically modified if the tetraloop-containing dsNA is going to be delivered without using lipid nanoparticles or some other delivery method that protects the dsNA from dégradation during the delivery process. However, in certain embodiments, one or more nucléotides are not modified.
Where the two substantially complementary strands of a dsRNA are comprised by separate RNA molécules, those molécules need not, but can be covalently connected. Where the two strands are connected covalently by means other than an uninterrupted chain of nucléotides between the 3’end of one strand and the 5’-end of the respective other strand forming the duplex structure, the connecting structure is referred to as a “linker.” The RNA strands may hâve the same or a different number of nucléotides. The maximum number of base pairs is the number of nucléotides in the shortest strand of the dsRNA minus any overhangs that are présent in the duplex. In addition to the duplex structure, an RNAi may comprise one or more nucléotide overhangs.
A dsRNA as described herein can further include one or more single-stranded nucléotide overhangs e.g., 1,2,3, or 4 nucléotides. dsRNAs having at least one nucléotide overhang can hâve unexpectedly superior inhibitory properties relative to their blunt-ended counterparts. A nucléotide overhang can comprise or consist of a nucleotide/nucleoside analog, including a deoxynucleotide/nucleoside. The overhang(s) can be on the sense strand, the antisense strand or any combination thereof. Furthermore, the nucleotide(s) of an overhang can be présent on the 5’-end, 3’end or both ends of either an antisense or sense strand of a dsRNA. In certain embodiments, longer, extended overhangs are possible.
A dsRNA can be synthesized by standard methods known in the art. iRNA compounds of the invention may be prepared using a two-step procedure. First, the individual strands of the double stranded RNA molécule are prepared separately. Then, the component strands are annealed. The individual strands of the siRNA compound can be prepared using solution-phase or solid-phase organic synthesis or both. In certain embodiments, the iRNA compound is produced from an expression vector delivered into a cell.
In one aspect, a dsRNA of the invention includes at least two nucléotide sequences, a sense sequence and an anti-sense sequence. The sense strand is selected from the group of sequences
provided in any one of the Tables in Appendix A, and the corresponding antisense strand of the sense strand is selected from the group of sequences of any one of the Tables m Appendix A.
In some embodiments, the sense strand is selected from the group of sequences provided in any one of the Tables in Appendix A, and the corresponding antisense strand of the sense strand is selected from the group of sequences of any one of the Tables in Appendix A. In this aspect, one of the two sequences is complementary to the other of the two sequences, with one of the sequences being substantially complementary to a sequence of an mRNA generated in the expression of an HBV gene. As such, in this aspect, a dsRNA will include two oligonucleotides, where one oligonucleotide is described as the sense strand in any one of the Tables in Appendix A and the second oligonucleotide is described as the corresponding antisense strand of the sense strand in any one of the Tables in Appendix A. In one embodiment, the substantially complementary sequences of the dsRNA are contained on separate oligonucleotides. In another embodiment, the substantially complementary sequences of the dsRNA are contained on a single oligonucleotide.
It is understood that, although some of the sequences in the Tables in Appendix A are described as modified or conjugated sequences, the RNA of the iRNA of the invention e.g., a dsRNA of the invention, may comprise any one of the sequences set forth in the Tables in Appendix A that is un-modified, unconjugated, or modified or conjugated differently than described therein. Additional target sites are provided, for example, in PCT Publication Nos. WO 2016/077321, WO 2012/024170, WO 2017/027350, and WO 2013/003520; and in Michler, 2016, the entire contents of wach of which are incorporated herein by reference.
The skilled person is well aware that dsRNAs having a duplex structure of about 20 to 23 base pairs, e.g., 21, base pairs hâve been hailed as particularly effective in inducing RNA interférence (Elbashir et al., EMBO 2001,20:6877-6888). However, others hâve found that shorter or longer RNA duplex structures can also be effective (Chu and Rana (2007) RNA 14:1714-1719; Kim et al. (2005) Nat Biotech 23:222-226). In the embodiments described above, by virtue of the nature of the oligonucleotide sequences provided in any one of the Tables in Appendix A, dsRNAs described herein can include at least one strand of a length of minimally 21 nucléotides. It can be reasonably expected that shorter duplexes having one of the sequences of any one of the Tables in Appendix A minus only a few nucléotides on one or both ends can be similarly effective as compared to the dsRNAs described above. Hence, dsRNAs having a sequence of at least 15,16,17,18,19,20, or more contiguous nucléotides derived from one of the sequences of any one of the Tables in Appendix A and differing in their ability to inhibit the expression of an HBV gene by not more than 5, 10,15, 20, 25, or 30 % inhibition from a dsRNA comprising the full sequence.
An iRNA as described herein can contain one or more mismatches to the target sequence, or to one or more HBV target sequences due, e.g., to sequence variations among the HBV génotypes. In one embodiment, an iRNA as described herein contains no more than 3 mismatches. If the antisense strand of the iRNA contains mismatches to a target sequence, it is préférable that the area of mismatch is not located in the center of the région of complementarity. If the antisense strand of the iRNA
contains mismatches to the target sequence, it is préférable that the mismatch be restricted to be withxn the last 5 nucléotides from either the 5 - or 3 -end of the région of complementanty. For example, for a 23 nucléotide iRNA agent the strand which is complementary to a région of an HBV gene, generally does not contain any mismatch within the central 13 nucléotides. The methods described herein or methods known in the art can be used to détermine whether an iRNA containing a mismatch to a target sequence is effective in inhibiting the expression of an HBV gene. Considération of the efïicacy of iRNAs with mismatches in inhibiting expression of an HBV gene is important, especially if the particular région of complementanty in an HBV gene is known to hâve polymorphie sequence variation within various génotypes and the population.
i. Modified iRNAs For Use in the Methods of the Invention
In some embodiments, the RNA of the iRNA for use in the invention e.g., a dsRNA, is unmodified, and does not comprise, e.g., Chemical modifications or conjugations known in the art and described herein, e.g., when produced from an expression vector. In other embodiments, the RNA of an iRNA of the invention, e.g., a dsRNA, is chemically modified to enhance stability or other bénéficiai characteristics. In certain embodiments of the invention, substantially ail of the nucléotides of an iRNA of the invention are modified. In other embodiments of the invention, ail of the nucléotides of an iRNA of the invention are modified. iRNAs of the invention in which “substantially ail of the nucléotides are modified” are largely but not wholly modified and can include not more than 5,4,3,2, or 1 unmodified nucléotides.
The nucleic acids featured in the invention can be synthesized or modified by methods well established in the art, such as those described in “Current protocols in nucleic acid chemistry,” Beaucage, S.L. et al. (Edrs.), John Wiley & Sons, Inc., New York, NY, USA, which is incorporated herein by reference. Modifications include, for example, end modifications, e.g., 5’-end modifications (phosphorylation, conjugation, inverted linkages) or 3’-end modifications (conjugation, DNA nucléotides, inverted linkages, etc.); base modifications, e.g., replacement with stabilizing bases, destabilizing bases, or bases that base pair with an expanded répertoire of partners, removal of bases (abasic nucléotides), or conjugated bases; sugar modifications (e.g., at the 2’-position or 4’position) or replacement of the sugar; or backbone modifications, including modification or replacement of the phosphodiester linkages. Spécifie examples of iRNA compounds usefiil in the embodiments described herein include, but are not limited to RNAs containing modified backbones or no naturel intemucleoside linkages. RNAs having modified backbones include, among others, those that do not hâve a phosphorus atom in the backbone. For the purposes of this spécification, and as sometimes referenced in the art, modified RNAs that do not hâve a phosphorus atom in their intemucleoside backbone can also be considered to be oligonucleosides. In some embodiments, a modified iRNA will hâve a phosphorus atom in its intemucleoside backbone.
Modified RNA backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl
phosphonates including 3’-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3’-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3’-5’ linkages, 2’-5’-linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3’-5’ to 5’-3’ or 2’-5’ to 5’2’. Varions salts, mixed salts and free acid forms are also included.
Représentative US patents that teach the préparation of the above phosphorus-containing linkages include, but are not limited to, US Patent Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,195; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939;
5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,316; 5,550,111; 5,563,253;
5,571,799; 5,587,361; 5,625,050; 6,028,188; 6,124,445; 6,160,109; 6,169,170; 6,172,209; 6,239,265; 6,277,603; 6,326,199; 6,346,614; 6,444,423; 6,531,590; 6,534,639; 6,608,035; 6,683,167; 6,858,715; 6,867,294; 6,878,805; 7,015,315; 7,041,816; 7,273,933; 7,321,029; and US Pat RE39464, the entire contents of each of which are hereby incorporated herein by reference.
Modified RNA backbones that do not include a phosphorus atom therein hâve backbones that are formed by short chain alkyl or cycloalkyl intemucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl intemucleoside linkages, or one or more short chain heteroatomic or heterocyclic intemucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones;
formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts.
Représentative US patents that teach the préparation of the above oligonucleosides include, 25 but are not limited to, US Patent Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141;
5,235,033; 5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307;
5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and, 5,677,439, the entire contents of each of which are hereby incorporated herein by reference.
In other embodiments, suitable RNA mimetics are contemplated for use in iRNAs, in which both the sugar and the intemucleoside linkage, i.e., the backbone, of the nucléotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an RNA mimetic that has been shown to hâve excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar backbone of an RNA is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Représentative US patents that teach the préparation of PNA compounds include, but are not limited to, US Patent Nos. 5,539,082; 5,714,331;
and 5,719,262, the entire contents of each of which are hereby incorporated herein by reference. Additional PNA compounds suitable for use in the iRNAs of the invention are described in, for example, inNielsen étal., Science, 1991,254, 1497-1500.
Some embodiments featured in the invention include RNAs with phosphorothioate backbones 5 and oligonucleosides with heteroatom backbones, and in particular -CHz-NH-CHz-, —CH2-N(CH3)O-CH2-[known as a methylene (methylimino) or MMI backbone], —CH2-O-N(CH3)-CH2—, — CHrN(CH3)-N(CH3)-CH2-and -N(CH3)-CH2-CH2-[wherein the native phosphodiester backbone is represented as -O-P-O-CHz—] of the above-referenced US Patent No. 5,489,677, and the amide backbones of the above-referenced US Patent No. 5,602,240. In some embodiments, the RNAs featured herein hâve morpholino backbone structures of the above-referenced US Patent No.
5,034,506.
Modified RNAs can also contain one or more substituted sugar moieties. The iRNAs, e.g., dsRNAs, featured herein can include one of the following at the 2’-position: OH; F; O-, S-, or Nalkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and 15 alkynyl can be substituted or unsubstituted Ci to Cio alkyl or C2 to Cio alkenyl and alkynyl.
Exemplary suitable modifications include O[(CH2)nO] mCH3, O(CH2).nOCHj, O(CH2)nNH2, O(CH2) nCH3,0(CH2)nONH2, and O(CH2)nON[(CH2)nCH3)]2, where n and m are from 1 to about 10. In other embodiments, dsRNAs include one of the following at the 2’ position: Ci to Cio lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, 20 OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an iRNA, or a group for improving the pharmacodynamie properties of an iRNA, and other substituents having similar properties. In some embodiments, the modification includes a 2’-methoxyethoxy (2’-O25 CH2CH2OCH3, also known as 2’-O-(2-methoxyethyl) or 2’-M0E) (Martin et al., Helv. Chim. Acta, 1995,78:486-504) i.e., an alkoxy-alkoxy group. Another exemplary modification is 2’dimethylaminooxyethoxy, i.e., a O(CH2)2ON(CH3)2 group, also known as 2’-DMAOE, as described in examples herein below, and 2’-dimethylaminoethoxyethoxy (also known in the art as 2’-Odimethylaminoethoxyethyl or 2’-DMAEOE), i.e., 2’-O-CH2-O-CH2-N(CH2)2.
Other modifications include 2’-methoxy (2’-OCH3), 2’-aminopropoxy (2’OCH2CH2CH2NH2) and 2’-fluoro (2’-F). Similar modifications can also be made at other positions on the RNA of an iRNA, particularly the 3’ position of the sugar on the 3’ terminal nucléotide or in 2’-5’ linked dsRNAs and the 5’ position of 5’ terminal nucléotide. iRNAs can also hâve sugar mimetics such as cyclobutyl moieties in place of the pentofiiranosyl sugar. Représentative US patents that teach 35 the préparation of such modified sugar structures include, but are not limited to, US Patent Nos.
4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134;
5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873;
5,670,633; and 5,700,920, certain of which are commonly owned with the instant application,. The entire contents of each of the foregoing are hereby incorporated herein by reference.
The RNA of an iRNA can also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodifîed” or “naturel” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and naturel nucleobases such as deoxythymine (dT), 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2aminoadenine, 6-methyl and other alkyl dérivatives of adenine and guanine, 2-propyl and other alkyl dérivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl anal other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-daazaadenine and 3-deazaguanine and 3-deazaadenine. Further nucleobases include those disclosed in US Patent No. 3,687,808, those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008; those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. L, ed. John Wiley & Sons, 1990, these disclosed by Englisch et aï., Angewandte Chemie, International Edition, 1991, 30,613, and those disclosed by Sanghvi, Y S., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Ed., CRC Press, 1993. Certain of these nucleobases are particularly usefiil for increasing the binding afïinity of the oligomeric compounds featured in the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5methylcytosine substitutions hâve been shown to increase nucleic acid duplex stability by 0.6-1.2°C (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., Eds., dsRNA Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are exemplary base substitutions, even more particularly when combined with 2’-O-methoxyethyl sugar modifications.
Représentative US patents that teach the préparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted US Patent Nos. 3,687,808,4,845,205; 5,130,30; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121,5,596,091; 5,614,617; 5,681,941; 5,750,692; 6,015,886; 6,147,200; 6,166,197; 6,222,025; 6,235,887; 6,380,368; 6,528,640; 6,639,062; 6,617,438; 7,045,610; 7,427,672; and 7,495,088, the entire contents of each of which are hereby incorporated herein by reference.
The RNA of an iRNA can also be modified to include one or more locked nucleic acids (LNA). A locked nucleic acid is a nucleptide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2' and 4' carbons. This structure effectively locks the ribose in the 3'-endo structural conformation. The addition of locked nucleic acids to siRNAs has
been shown to increase siRNA stability in sérum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(l):439-447; Mook, OR. et al., (2007) Mol Cane Ther 6(3):833843; Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193).
In some embodiments, the iRNA of the invention comprises one or more monomers that are
UNA (unlocked nucleic acid) nucléotides. UNA is unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked sugar residue. In one example, UNA also encompasses monomer with bonds between d'-C4' hâve been removed (i.e. the covalent carbonoxygen-carbon bond between the Cl' and C4' carbons). In another example, the C2'-C3' bond (i.e. the covalent carbon-carbon bond between the C2' and C3' carbons) of the sugar has been removed (see
Nue. Acids Symp. Sériés, 52, 133-134 (2008) and Fluiter et al., Mol. Biosyst., 2009, 10, 1039 hereby incorporated by reference).
The RNA of an iRNA can also be modified to include one or more bicyclic sugar moitiés. A “bicyclic sugar” is a furanosyl ring modified by the bridging of two atoms. A“bicyclic nucleoside”(“BNA”) is a nucleoside having a sugar moiety comprising a bridge connecting two carbon atoms of the sugar ring, thereby forming a bicyclic ring system. In certain embodiments, the bridge connects the 4'-carbon and the 2'-carbon of the sugar ring. Thus, in some embodiments an agent of the invention may include one or more locked nucleic acids (LNA). A locked nucleic acid is a nucléotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2’ and 4’ carbons. In other words, an LNA is a nucléotide comprising a bicyclic sugar moiety comprising a 4’-CH2-O-2’ bridge. This structure effectively “locks” the ribose in the 3’-endo structural conformation. The addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in sérum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(l):439-447; Mook, OR. Et al., (2007) Mol Cane Ther 6(3):833-843; Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193). Examples of bicyclic nucleosides for use in the polynucleotides of the invention include without limitation nucleosides comprising a bridge between the 4' and the 2' ribosyl ring atoms. In certain embodiments, the antisense polynucleotide agents of the invention include one or more bicyclic nucleosides comprising a 4' to 2' bridge. Examples of such 4' to 2' bridged bicyclic nucleosides, include but are not limited to 4'-(CH2)—O-2' (LNA); 4'-(CH2)—S-2'; 4'-(CH2)2—0-2' (ENA); 4'-CH(CH3)—0-2' (also referred to as “constrained ethyl” or “cEt”) and 4'-CH(CH2OCH3)—O-2' (and analogs thereof; see, e.g., US Patent
No. 7,399,845); 4'-C(CH3)(CH3)—O-2' (and analogs thereof; see e.g., US Patent No. 8,278,283); 4'CH2—N(OCH3)-2' (and analogs thereof; see e.g., US Patent No. 8,278,425); 4'-CH2—O—N(CH3)2' (see, e.g.,US2004017I570); 4'-CH2—N(R)—0-2', wherein R is H, C1-C12 alkyl, or a protecting group (see, e.g., US Patent No. 7,427,672); 4'-CH2—C(H)(CH3)-2' (see, e.g., Chattopadhyaya et al.,
J. Org. Chem., 2009, 74, 118-134); and 4'-CH2—C(=CH2)-2' (and analogs thereof; see, e.g., US Patent No. 8,278,426). The entire contents of each of the foregoing are hereby incorporated herein by reference.
Additional représentative US patents and US patent publications that teach the préparation of locked nucleic acid nucléotides include, but are not limited to, the following: US Patent Nos.
6,268,490; 6,525,191; 6,670,461; 6,770,748; 6,794,499; 6,998,484; 7,053,207; 7,034,133;7,084,125; 7,399,845; 7,427,672; 7,569,686; 7,741,457; 8,022,193; 8,030,467; 8,278,425; 8,278,426; 8,278,283; US 20080039618; and US 20090012281, the entire contents of each of which are hereby incorporated herein by reference.
Any of the foregoing bicyclic nucleosides can be prepared having one or more stereochemical sugar configurations including for example a-L-ribofuranose and β-D-ribofuranose (see WO 99/14226).
The RNA of an iRNA can also be modified to include one or more constrained ethyl nucléotides. As used herein, a constrained ethyl nucléotide or cEt is a locked nucleic acid comprising a bicyclic sugar moiety comprising a 4'-CH(CH3)-O-2' bridge. In one embodiment, a constrained ethyl nucléotide is in the S conformation referred to herein as “S-cEt.”
An iRNA of the invention may also include one or more “conformationally restricted nucléotides” (“CRN”). CRN are nucléotide analogs with a linker connecting the C2’and C4’ carbons of ribose or the C3 and -C5’ carbons of ribose. CRN lock the ribose ring into a stable conformation and increase the hybridization affinity to mRNA. The linker is of suffîcient length to place the oxygen in an optimal position for stability and affinity resulting in less ribose ring puckering.
Représentative publications that teach the préparation of certain of the above noted CRN include, but are not limited to, US 20130190383 and WO 2013036868, the entire contents of each of which are hereby incorporated herein by reference.
Potentially stabilizing modifications to the ends of RNA molécules can include N(acetylaminocaproyI)-4-hydroxyprolinol (Hyp-C6-NHAc), N-(caproyl-4-hydroxyprolinol (Hyp-C6), N-(acetyl-4-hydroxyprolinol (Hyp-NHAc), thymidine-2'-0-deoxythymidine (ether), N(aminocaproyl)-4-hydroxyprolinol (Hyp-C6-amino), 2-docosanoyl-uridine-3- phosphate, inverted base dT(idT) and others. Disclosure of this modification can be found in WO 2011005861.
Other modifications of the nucléotides of an iRNA of the invention include a 5’ phosphate or 5’ phosphate mimic, e.g., a 5’-terminal phosphate or phosphate mimic on the antisense strand of an RNAi agent. Suitable phosphate mimics are disclosed in, for example US20120157511, the entire contents of which are incorporated herein by reference. - In certain spécifie embodiments, the RNAi agent for use in the methods of the invention is an agent selected from the group of agents listed in any one of the Tables in Appendix A. These agents may further comprise a ligand.
ii. iRNAs Conjugated to Ligands
Another modification of the RNA of an iRNA of the invention involves chemically linking to the RNA one or more ligands, moieties or conjugales that enhance the activity, cellular distribution, or cellular uptake of the iRNA. Such moieties include but are not limited to lipid moieties such as a
cholestérol moiety (Letsinger et al., Proc. Natl. Acid. Sci. USA, 1989, 86: 6553-6556), cholic acid (Manoharan et al., Biorg. Med. Chem. Let., 1994,4:1053-1060), a thioether, e.g., beryl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660:306-309; Manoharan et al., Biorg. Med. Chem. Let., 1993,3:2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992,20:533-538), an 5 aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J, 1991, 10:1111-1118; Kabanovef al., FEBSLett., 1990, 259:327-330; Svinarchuk et al., Biochimie, 1993, 75:49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecylrac-glycero-3-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36:3651-3654; Shea et al., Nucl. Acids Res., 1990, 18:3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., 10 Nucleosides & Nucléotides, 1995,14:969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36:3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995,1264:229-237), or an octadecylamine or hexylamino-carbonyloxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996,277:923-937).
In one embodiment, a ligand alters the distribution, targeting, or lifetime of an iRNA agent 15 into which it is incorporated. In preferred embodiments a ligand provides an enhanced affinity for a selected target, e.g., molécule, cell or cell type, compartment, e.g., a cellular or organ compartment, tissue, organ or région of the body, as, e.g., compared to a species absent such a ligand. Preferred ligands will not take part in duplex pairing in a duplexed nucleic acid.
Ligands can include a naturally occurring substance, such as a protein (e.g., human sérum 20 albumin (HSA), low-density lipoprotein (LDL), or globulin); carbohydrate (e.g., a dextran, pullulan, chitin, chitosan, inulin, cyclodextrin, N-acetylgalactosamine, or hyaluronic acid); or a lipid. The ligand can also be a recombinant or synthetic molécule, such as a synthetic polymer, e.g., a synthetic polyamino acid. Examples of polyamino acids include polyamino acid is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydride copolymer, poly(L-lactide25 co-glycolied) copolymer, divinyl ether-maleic anhydride copolymer, N-(2hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyuréthane, poly(2-ethylacryllic acid), N-isopropylacrylamide polymers, or polyphosphazine. Example of polyamines include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine, pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, 30 arginine, amidine, protamine, cationic lipid, cationic porphyrin, quatemary sait of a polyamine; or an alpha helical peptide. ~
Ligands can also include targeting groups, e.g., a cell or tissue targeting agent, e.g., a lectin, glycoprotein, lipid, or protein, e.g., an antibody, that binds to a specified cell type such as a kidney ’ cell. A targeting group can be a thyrotropin, melanotropin, lectin, glycoprotein, surfactant protein A, 35 Mucin carbohydrate, multivalent lactose, monovalent or multivalent galactose, N-acetylgalactosamine, N-acetyl-gulucoseamine multivalent mannose, multivalent fucose, glycosylated polyaminoacids, transferrin, bisphosphonate, polyglutamate, polyaspartate, a lipid, cholestérol, a steroid, bile acid, folate, vitamin B12, vitamin A, biotin, or an RGD peptide or RGD peptide mimetic.
In certain embodiments, ligands include monovalent or multivalent galactose. In certain embodiments, ligands include cholestérol.
Other examples of ligands include dyes, intercalating agents (e.g. acridines), cross-linkers (e.g. psoralene, mitomycin C), porphyrins (TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic hydrocarbons (e.g., phenazine, dihydrophenazine), artifïcial endonucleases (e.g. EDTA), lipophilie molécules, e.g., cholestérol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, bomeol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid,03(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine)and peptide conjugales (e.g., antennapedia peptide, Tat peptide), alkylating agents, phosphate, amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG]?, polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes, haptens (e.g. biotin), transport/absorption facilitators (e.g., aspirin, vitamin E, folie acid), synthetic ribonucleases (e.g., imidazole, bisimidazole, histamine, imidazole clusters, acridineimidazole conjugales, Eu3+ complexes of tetraazamacrocycles), dinitrophenyl, HRP, or AP.
Ligands can be proteins, e.g., glycoproteins, or peptides, e.g., molécules having a spécifie afïinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a hepatic cell. Ligands can also include hormones and hormone receptors. They can also include nonpeptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, multivalent lactose, monovalent or multivalent galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose, or multivalent fucose. The ligand can be, for example, a lipopolysaccharide, an activator of p38 MAP kinase, or an activator of NF-kB.
The ligand can be a substance, e.g., a drug, which can increase the uptake of the iRNA agent into the cell, for example, by disrupting the cell’s cytoskeleton, e.g., by disrupting the cell’s microtubules, microfilaments, or intermediate filaments. The drug can be, for example, taxon, vincristine, Vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or myoservin.
In some embodiments, a ligand attached to an iRNA as described herein acts as a pharmacokinetic modulator (PK modulator). PK modulators include lipophiles, bile acids, steroids, phospholipid analogues, peptides, protein binding agents, PEG, vitamins etc. Exemplary PK modulators include, but are not limited to, cholestérol, fatty acids, cholic acid, lithocholic acid, dialkylglycerides, diacylglyceride, phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotin etc. Oligonucleotides that comprise a number ofphosphorothioate linkages are also known to bind to sérum protein, thus short oligonucleotides, e.g., oligonucleotides of about 5 bases, 10 bases, 15 bases or 20 bases, comprising multiple ofphosphorothioate linkages in the backbone are also amenable to the présent invention as ligands (e.g. as PK modulating ligands). In addition, aptamers that bind sérum components (e.g. sérum proteins) are also suitable for use as PK modulating ligands in the embodiments described herein.
Ligand-conjugated oligonucleotides of the invention may be synthesized by the use of an oligonucleotide that bears a pendant reactive functionality, such as that derived from the attachment of a linking molécule onto the oligonucleotide (described below). This reactive oligonucleotide may be reacted directly with commercially-available ligands, ligands that are synthesized bearing any of a variety of protecting groups, or ligands that hâve a linking moiety attached thereto.
The oligonucleotides used in the conjugales of the présent invention may be conveniently and routinely made through the well-known technique of solid-phase synthesis. Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art may additionally or alternatively be employed. It is also known to use similar techniques to préparé other oligonucleotides, such as the phosphorothioates and alkylated dérivatives.
In the ligand-conjugated oligonucleotides and ligand-molecule bearing sequence-specifîc linked nucleosides of the présent invention, the oligonucleotides and oligonucleosides may be assembled on a suitable DNA synthesizer utilizing standard nucléotide or nucleoside precursors, or nucléotide or nucleoside conjugale precursors that already bear the linking moiety, ligand-nucleotide or nucleoside-conjugate precursors that already bear the ligand molécule, or non-nucleoside ligandbearing building blocks.
When using nucleotide-conjugate precursors that already bear a linking moiety, the synthesis of the sequence-specific linked nucleosides is typically completed, and the ligand molécule is then reacted with the linking moiety to form the ligand-conjugated oligonucleotide. In some embodiments, the oligonucleotides or linked nucleosides of the présent invention are synthesized by an automated synthesizer using phosphoramidites derived from ligand-nucleoside conjugales in addition to the standard phosphoramidites and non-standard phosphoramidites that are commercially available and routinely used in oligonucleotide synthesis.
1. Lipid Conjugates
In one embodiment, the ligand or conjugale is a lipid or lipid-based molécule. Such a lipid or lipid-based molécule preferably binds a sérum protein, e.g., human sérum albumin (HSA). An HSA binding ligand allows for distribution of the conjugale to a target tissue, e.g., a non-kidney target tissue of the body. For example, the target tissue can be the liver, including parenchymal cells of the liver. Other molécules that can bind HSA can also be used as ligands. For example, naproxen or aspirin can be used. A lipid or lipid-based ligand can (a) increase résistance to dégradation of the conjugale, (b) increase targeting or transport into a target cell or cell membrane, or (c) can be used to adjust binding to a sérum protein, e.g., HSA.
A lipid based ligand can be used to inhibit, e.g., control the binding of the conjugale to a target tissue. For example, a lipid or lipid-based ligand that binds to HSA more strongly will be less likely to be targeted to the kidney and therefore less likely to be cleared from the body. A lipid or lipid-based ligand that binds to HSA less strongly can be used to target the conjugale to the kidney.
In a preferred embodiment, the lipid based ligand binds HSA. Preferably, it binds HSA with a sufficient affinity such that the conjugate will be preferably distributed to a non-kidney tissue. However, it is preferred that the affinity not be so strong that the HSA-ligand binding cannot be reversed.
In another preferred embodiment, the lipid based ligand binds HSA weakly or not at ail, such that the conjugate will be preferably distributed to the kidney. Other moieties that target to kidney cells can also be used in place of or in addition to the lipid based ligand.
In another aspect, the ligand is a moiety, e.g., a vitamin, which is taken up by a target cell, e.g., a proliferating cell. These are particularly usefiil for treating disorders characterized by unwanted cell prolifération, e.g., of the malignant or non-malignant type, e.g., cancer cells. Exemplary vitamins include vitamin A, E, and K. Other exemplary vitamins include are B vitamin, e.g., folie acid, B12, riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up by target cells such as liver cells. Also included are HSA and low density lipoprotein (LDL).
2. Cell Perméation Agents
In another aspect, the ligand is a cell-permeation agent, preferably a helical cell-permeation agent. Preferably, the agent is amphipathic. An exemplary agent is a peptide such as tat or antennopedia. If the agent is a peptide, it can be modified, including a peptidylmimetic, invertomers, non-peptide or pseudo-peptide linkages, and use of D-amino acids. The helical agent is preferably an 20 alpha-helical agent, which preferably has a lipophilie and a lipophobic phase.
The ligand can be a peptide or peptidomimetic. A peptidomimetic (also referred to herein as an oligopeptidomimetic) is a molécule capable of folding into a defined three-dimensional structure similar to a natural peptide. The attachment of peptide and peptidomimetics to iRNA agents can affect pharmacokinetic distribution of the iRNA, such as by enhancing cellular récognition and absorption. The peptide or peptidomimetic moiety can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35,40,45, or 50 amino acids long.
A peptide or peptidomimetic can be, for example, a cell perméation peptide, cationic peptide, amphipathic peptide, or hydrophobie peptide (e.g., consisting primarily of Tyr, Trp or Phe). The peptide moiety can be a dendrimer peptide, constrained peptide or crosslinked peptide. In another 30 alternative, the peptide moiety can include a hydrophobie membrane translocation sequence (MTS).
An exemplary hydrophobie MTS-containing peptide is RFGF having the amino acid sequence AAVALLPAVLLALLAP (SEQ ID NO: 33). An RFGF analogue (e.g., amino acid sequence AALLPVLLAAP (SEQ ID NO: 34) containing a hydrophobie MTS can also be a targeting moiety. The peptide moiety can be a “delivery” peptide, which can carry large polar molécules including peptides, oligonucleotides, and protein across cell membranes. For example, sequences from the HIV Tat protein (GRKKRRQRRRPPQ (SEQ ID NO: 35) and the Drosophila Antennapedia protein (RQIKIWFQNRRMKWKK (SEQ ID NO: 36) hâve been found to be capable of functioning as delivery peptides. A peptide or peptidomimetic can be encoded by a random sequence of DNA, such as a peptide identifïed from a phage-display library, or one-bead-one-compound (OBOC) combinatorial library (Lam et al., Nature, 354:82-84, 1991). Examples of a peptide or peptidomimetic tethered to a dsRNA agent via an incorporated monomer unit for cell targeting purposes is an arginine-glycine-aspartic acid (RGD)-peptide, or RGD mimic. A peptide moiety can range in length from about 5 amino acids to about 40 amino acids. The peptide moieties can hâve a structural modification, such as to increase stability or direct conformational properties. Any of the structural modifications described below can be utilized.
An RGD peptide for use in the compositions and methods of the invention may be linear or cyclic, and may be modified, e.g., glycosylated or methylated, to facilitate targeting to a spécifie tissue(s). RGD-containing peptides and peptidiomimemtics may include D-amino acids, as well as synthetic RGD mimics. In addition to RGD, one can use other moieties that target the integrin ligand. Preferred conjugales of this ligand target PECAM-1 or VEGF.
A “cell perméation peptide” is capable of permeating a cell, e.g., a microbial cell, such as a bacterial or fungal cell, or a mammalian cell, such as a human cell. A microbial cell-permeating peptide can be, for example, an α-helical linear peptide (e.g., LL-37 or Ceropin PI), a disulfide bondcontaining peptide (e.g., a -defensin, β-defensin or bactenecin), or a peptide containing only one or two dominating amino acids (e.g., PR-39 or indolicidin). A cell perméation peptide can also include a nuclear localization signal (NLS). For example, a cell perméation peptide can be a bipartite amphipathic peptide, such as MPG, which is derived from the fusion peptide domain of HTV-1 gp41 and the NLS of SV40 large T antigen (Simeoni et al., Nucl. Acids Res. 31:2717-2724,2003).
3. Carbohydrate Conjugates
In some embodiments of the compositions and methods of the invention, an iRNA oligonucleotide further comprises a carbohydrate. The carbohydrate conjugated iRNA are advantageous for the in vivo delivery of nucleic acids, as well as compositions suitable for in vivo therapeutic use, as described herein. As used herein, “carbohydrate” refers to a compound which is either a carbohydrate perse made up of one or more monosaccharide units having at least 6 carbon atoms (which can be linear, branched or cyclic) with an oxygen, nitrogen or sulfur atom bonded to each carbon atom; or a compound having as a part thereof a carbohydrate moiety made up of one or more monosaccharide units each having at least six carbon atoms (which can be linear, branched or cyclic), with an oxygen, nitrogen or sulfur atom bonded to each carbon atom. Représentative carbohydrates include the sugars (mono-, di-, tri- and oligosaccharides containing from about 4,5, 6, 7, 8, or 9 monosaccharide units), and polysaccharides such as starches, glycogen, cellulose and polysaccharide gums. Spécifie monosaccharides include C5 and above (e.g., C5, C6, C7, or C8) sugars; di- and trisaccharides include sugars having two or three monosaccharide units (e.g., C5, C6, C7, or C8).
In one embodiment, a carbohydrate conjugale for use in the compositions and methods of the invention is a monosaccharide. In another embodiment, a carbohydrate conjugale for use in the compositions and methods of the invention is selected from the group consisting of: HO /OH
NHAc Formula IV,
H Formula ΙΠ,
NHAc Formula V,
HO ,OH
HO OH NHAc °
NHAc o Formula VI,
NHAc Formula VII,
O Formula XII,
In one embodiment, the monosaccharide is an N-acetylgalactosamine, such as
Another représentative carbohydrate conjugale for use in the embodiments described herein includes, but is not limited to, HO z0H
(Formula ΧΧΙΠ), when one of X or Y is an oligonucleotide, the other is a hydrogen.
In certain embodiments of the invention, the GalNAc or GalNAc dérivative is attached to an iRNA agent of the invention via a monovalent linker. In some embodiments, the GalNAc or GalNAc dérivative is attached to an iRNA agent of the invention via a bivalent linker. In yet other embodiments of the invention, the GalNAc or GalNAc dérivative is attached to an iRNA agent of the 10 invention via a trivalent linker.
In one embodiment, the double stranded RNAi agents of the invention comprise one GalNAc or GalNAc dérivative attached to the iRNA agent. In another embodiment, the double stranded RNAi agents of the invention comprise a plurality (e.g., 2, 3,4,5, or 6) GalNAc or GalNAc dérivatives, each independently attached to a plurality of nucléotides of the double stranded RNAi 15 agent through a plurality of monovalent linkers.
In some embodiments, for example, when the two strands of an iRNA agent of the invention are part of one larger molécule connected by an uninterrupted chain of nucléotides between the 3’-end of one strand and the 5’-end of the respective other strand forming a hairpin loop comprising, a plurality of unpaired nucléotides, each unpaired nucléotide within the hairpin loop may independently 20 comprise a GalNAc or GalNAc dérivative attached via a monovalent linker. The hairpin loop may also be formed by an extended overhang in one strand of the duplex.
In some embodiments, the carbohydrate conjugale further comprises one or more additional ligands as described above, such as, but not limited to, a PK modulator or a cell perméation peptide.
Additional carbohydrate conjugales suitable for use in the présent invention include those described in WO 2014179620 and WO 2014179627, the entire contents of each of which are 5 incorporated herein by reference.
4. Linkers
In some embodiments, the conjugale or ligand described herein can be attached to an iRNA oligonucleotide with various linkers that can be cleavable or non-cleavable.
The term linker or “linking group” means an organic moiety that connects two parts of a compound, e.g., covalently attaches two parts of a compound. Linkers typically comprise a direct bond or an atom such as oxygen or sulfur, a unit such as NR8, C(O), C(O)NH, SO, SO2, SO2NH or a chain of atoms, such as, but not limited to, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, arylalkyl, arylalkenyl, arylalkynyl, heteroarylalkyl, heteroarylalkenyl, heteroarylalkynyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, aryl, heteroaryl, heterocyclyl, cycloalkyl, cycloalkenyl, alkylarylalkyl, alkylarylalkenyl, alkylarylalkynyl, alkenylarylalkyl, alkenylarylalkenyl, alkenylarylalkynyl, alkynylarylalkyl, alkynylarylalkenyl, alkynylarylalkynyl, alkylheteroarylalkyl, alkylheteroarylalkenyl, alkylheteroarylalkynyl, alkenylheteroarylalkyl, alkenylheteroarylalkenyl, alkenylheteroarylalkynyl, 20 alkynylheteroarylalkyl, alkynylheteroarylalkenyl, alkynylheteroarylalkynyl, alkylheterocyclylalkyl, alkylheterocyclylalkenyl, alkylhererocyclylalkynyl, alkenylheterocyclylalkyl, alkenylheterocyclylalkenyl, alkenylheterocyclylalkynyl, alkynylheterocyclylalkyl, alkynylheterocyclylalkenyl, alkynylheterocyclylalkynyl, alkylaryl, alkenylaryl, alkynylaryl, alkylheteroaryl, alkenylheteroaryl, alkynylhereroaryl, which one or more methylenes can be interrupted or terminated by O, S, S(O), SO2, N(R8), C(O), substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocyclic; where R8 is hydrogen, acyl, aliphatic or substituted aliphatic. In one embodiment, the linker is about 1-24 atoms, 2-24, 3-24,4-24, 5-24, 6-24, 6-18,7-18, 8-18 atoms, 7-17, 8-17, 6-16, 7-16, or 8-16 atoms.
A cleavable linking group is one which is sufficiently stable outside the cell, but which upon 30 entry into a target cell is cleaved to release the two parts the linker is holding together. In a preferred embodiment, the cleavable linking group is cleaved at least about 10 times, 20, times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90 times or more, or at least about 100 times faster in a target cell or under a first reference condition (which can, e.g., be selected to mimic or represent intracellular conditions) than in the blood of a subject, or under a second reference condition (which 35 can, e.g., be selected to mimic or represent conditions found in the blood or sérum).
Cleavable linking groups are susceptible to cleavage agents, e.g., pH, redox potential or the presence of degradative molécules. Generally, cleavage agents are more prévalent or found at higher levels or activities inside cells than in sérum or blood. Examples of such degradative agents include:
redox agents which are selected for particular substrates or which hâve no substrate specificity, including, e.g., oxidative or reductive enzymes or reductive agents such as mercaptans, présent in cells, that can dégradé a redox cleavable linking group by réduction; esterases; endosomes or agents that can create an acidic environment, e.g., those that resuit in a pH of five or lower; enzymes that can 5 hydrolyze or dégradé an acid cleavable linking group by acting as a general acid, peptidases (which can be substrate spécifie), and phosphatases.
A cleavable linkage group, such as a disulfîde bond can be susceptible to pH. The pH of human sérum is 7.4, while the average intracellular pH is slightly lower, ranging from about 7.1-7.3. Endosomes hâve a more acidic pH, in the range of 5.5-6.0, and lysosomes hâve an even more acidic 10 pH at around 5.0. Some linkers will hâve a cleavable linking group that is cleaved at a preferred pH, thereby releasing a cationic lipid from the ligand inside the cell, or into the desired compartment of the cell. .
A linker can include a cleavable linking group that is cleavable by a particular enzyme. The type of cleavable linking group incorporated into a linker can dépend on the cell to be targeted. For 15 example, a liver-targeting ligand can be linked to a cationic lipid through a linker that includes an ester group. Liver cells are rich in esterases, and therefore the linker will be cleaved more efficiently in liver cells than in cell types that are not esterase-rich. Other cell-types rich in esterases include cells of the lung, rénal cortex, and testis.
Linkers that contain peptide bonds can be used when targeting cell types rich in peptidases, 20 such as liver cells and synoviocytes.
In general, the suitability of a candidate cleavable linking group can be evaluated by testing the ability of a degradative agent (or condition) to cleave the candidate linking group. It will also be désirable to also test the candidate cleavable linking group for the ability to resist cleavage in the blood or when in contact with other non-target tissue. Thus, one can détermine the relative susceptibility to cleavage between a first and a second condition, where the first is selected to be indicative of cleavage in a target cell and the second is selected to be indicative of cleavage in other tissues or biological fluids, e.g., blood or sérum. The évaluations can be carried out in cell free Systems, in cells, in cell culture, in organ or tissue culture, or in whole animais. It can be useful to make initial évaluations in cell-free or culture conditions and to confirm by further évaluations in whole animais. In preferred embodiments, useful candidate compounds are cleaved at least about 2, 4,10, 20, 30,40, 50, 60, 70, 80, 90, or about 100 times faster in the cell (or under in vitro conditions selected to mimic intracellular conditions) as compared to blood or sérum (or under in vitro conditions selected to mimic extracellular conditions).
a. Redox cleavable linking groups
In one embodiment, a cleavable linking group is a redox cleavable linking group that is cleaved upon réduction or oxidation. An example of reductively cleavable linking group is a disulphide linking group (-S-S-). To détermine if a candidate cleavable linking group is a suitable “reductively cleavable linking group,” or for example is suitable for use with a particular iRNA
moiety and particular targeting agent one can look to methods described herein. For example, a candidate can be evaluated by incubation with dithiothreitol (DTT), or other reducing agent using reagents know in the art, which mimic the rate of cleavage which would be observed in a cell, e.g., a target cell. The candidates can also be evaluated under conditions which are selected to mimic blood or sérum conditions. In one, candidate compounds are cleaved by at most about 10% in the blood. In other embodiments, useful candidate compounds are degraded at least about 2,4,10,20,30,40,50, 60,70, 80,90, or about 100 times faster in the cell (or under in vitro conditions selected to mimic intracellular conditions) as compared to blood (or under in vitro conditions selected to mimic extracellular conditions). The rate of cleavage of candidate compounds can be determined using standard enzyme kinetics assays under conditions chosen to mimic intracellular media and compared to conditions chosen to mimic extracellular media.
b. Phosphate-based cleavable linking groups
In another embodiment, a cleavable linker comprises a phosphate-based cleavable linking group. A phosphate-based cleavable linking group is cleaved by agents that dégradé or hydrolyze the phosphate group. An example of an agent that cleaves phosphate groups in cells are enzymes such as phosphatases in cells. Examples of phosphate-based linking groups are -O-P(O)(ORk)-O-, -OP(S)(ORk)-O-, -O-P(S)(SRk)-O-, -S-P(O)(ORk)-O-, -O-P(O)(ORk)-S-, -S-P(O)(ORk)-S-, -OP(S)(ORk)-S-, -S-P(S)(ORk)-O-, -O-P(O)(Rk)-O-, -O-P(S)(Rk)-O-, -S-P(O)(Rk)-O-, -S-P(S)(Rk)-O-, -S-P(O)(Rk)-S-, -O-P(S)( Rk)-S-. Preferred embodiments are -O-P(O)(OH)-O-, -O-P(S)(OH)-O-, -OP(S)(SH)-O-, -S-P(O)(OH)-O-, -O-P(O)(OH)-S-, -S-P(O)(OH)-S-, -O-P(S)(OH)-S-, -S-P(S)(OH)-O-, -O-P(O)(H)-O-, -O-P(S)(H)-O-, -S-P(O)(H)-O, -S-P(S)(H)-O-, -S-P(O)(H)-S-, -O-P(S)(H)-S-, A preferred embodiment is -O-P(O)(OH)-O-. These candidates can be evaluated using methods analogous to those described above.
c. Acid cleavable linking groups
In another embodiment, a cleavable linker comprises an acid cleavable linking group. An acid cleavable linking group is a linking group that is cleaved under acidic conditions. In preferred embodiments acid cleavable linking groups are cleaved in an acidic environment with a pH of about 6.5 or lower (e.g., about 6.0,5.75,5.5,5.25,5.0, or lower), or by agents such as enzymes that can act as a general acid. In a cell, spécifie low pH organelles, such as endosomes and lysosomes can provide a cleaving environment for acid cleavable linking groups. Examples of acid cleavable linking groups include but are not limited to hydrazones, esters, and esters of amino acids. Acid cleavable groups can hâve the general formula -C=NN-, C(O)O, or -OC(O). A preferred embodiment is when the carbon attached to the oxygen of the ester (the alkoxy group) is an aryl group, substituted alkyl group, or tertiary alkyl group such as dimethyl pentyl or t-butyl. These candidates can be evaluated using methods analogous to those described above.
d. Ester-based linking groups
In another embodiment, a cleavable linker comprises an ester-based cleavable linking group. An ester-based cleavable linking group is cleaved by enzymes such as esterases and amidases in cells.
Examples of ester-based cleavable linking groups include but are not limited to esters of alkylene, alkenylene and alkynylene groups. Ester cleavable linking groups hâve the general formula -C(O)O-, or -OC(O)-. These candidates can be evaluated using methods analogous to those described above.
e. Peptide-based cïeaving groups
In yet another embodiment, a cleavable linker comprises a peptide-based cleavable linking group. A peptide-based cleavable linking group is cleaved by enzymes such as peptidases and proteases in cells. Peptide-based cleavable linking groups are peptide bonds formed between amino acids to yield oligopeptides (e.g., dipeptides, tripeptides etc.) and polypeptides. Peptide-based cleavable groups do not include the amide group (-C(O)NH-). The amide group can be formed between any alkylene, alkenylene or alkynelene. A peptide bond is a spécial type of amide bond formed between amino acids to yield peptides and proteins. The peptide based cleavage group is generally limited to the peptide bond (i.e., the amide bond) formed between amino acids yielding peptides and proteins and does not include the entire amide functional group. Peptide-based cleavable linking groups hâve the general formula - NHCHRAC(O)NHCHRBC(O)-, where RA and RB are the R groups of the two adjacent amino acids. These candidates can be evaluated using methods analogous to those described above.
In one embodiment, an iRNA of the invention is conjugated to a carbohydrate through a linker. Non-Iimiting examples of iRNA carbohydrate conjugales with linkers of the compositions and methods of the invention include, but are not limited to,
(Formula XXVIII),
(Formula XXX), and
(Formula XXXI), when one of X or Y is an oligonucleotide, the other is a hydrogen.
In certain embodiments of the compositions and methods of the invention, a ligand is one or more “GalNAc” (N-acetylgalactosamine) dérivatives attached through a bivalent or trivalent branched linker.
In one embodiment, a dsRNA of the invention is conjugated to a bivalent or trivalent branched linker selected from the group of structures shown in any of formula (XXXII) — (XXXV):
Formula XXXII
Formula XXXIII
p2A_Q2A_p2A p2B_Q2B_p2B _______-]-2A_|_2A q2A y2B |_2B ^^p3A_Q3A_j^3A */W N \ p3B_Q3B_p3B q3A γ3Α_|_3Α q3B
-j-3B_]_3B
p4B_Q4B_p4B y4A_[^4A q4A γ4Β^4Β q4B
p5A_Q5A_p5A •j~5A[^5A q5A — — p5B_Q5B_jj5B Jq5B p5C_Q5C_p5C ____
Jqîc
Formula XXXIV Formula XXXV wherein: q2A, q2B, q3A, q3B, q4A, q4B, q5A, q5B and q5C represent independently for each occurrence 0-20 and wherein the repeating unit can be the same or different;
p’A, p2B, p3A, p3B p4A p4B p5A p5B p5C -p2A ψ2Β ψ3Α p3B qMA ·ρ4Β qMA p5B pSC afe each 20 independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O), CH2, CH2NH or CH2O;
q2a, q:b, q3a, q3b, q4a, q4b, qsa, qsb, qsc are jndependently for each occurrence absent, alkylene, substituted alkylene wherin one or more methylenes can be interrupted or terminated by one or more of O, S, S(O), SO2) N(RN), C(R’)=C(R”), C^C or C(O);
R2a, R10 * * * * 15 * * * * 20 * * * * 25 * * 2B * 30, R3A, R3b, R4a, R4B, R5A, R5B, R5C are each independently for each occurrence absent, NH, O, O
HO-1^
H ü
S, CH2, C(O)O, C(O)NH, NHCH(Ra)C(O), -C(O)-CH(Ra)-NH-, CO, CH=N-O, ° s-s. S-S,
s—s or heterocyclyl;
L2A, L2B, L3A, L3B, L4A, L4B, L5A, L5B and L5C represent the ligand; i.e. each independently for each occurrence a monosaccharide (such as GalNAc), disaccharide, trisaccharide, tetrasaccharide, oligosaccharide, or polysaccharide; andRa is H or amino acid side chain.Trivalent conjugating GalNAc dérivatives are particularly usefiil for use with RNAi agents for inhibiting the expression of a target gene, such as those of formula (XXXV):
Formula XXXV
p5A_Q5A_p5A y5A_ |_5A .5A p5B_Q5B_p5B p5C_Q5C_p5C q5C ,
wherein L5A, L5B and L5C represent a monosaccharide, such as GalNAc dérivative.
Examples of suitable bivalent and trivalent branched linker groups conjugating GalNAc dérivatives include, but are not limited to, the structures recited above as formulas Π, VII, XI, X, and
XIII.
Représentative US patents that teach the préparation of RNA conjugales include, but are not limited to, US Patent Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;
5,552,538; 5,578,717,5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603;
5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941;
4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963;
5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241,
5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142;
5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941; 6,294,664;
6,320,017; 6,576,752; 6,783,931; 6,900,297; 7,037,646; 8,106,022, the entire contents of each of which are hereby incorporated herein by reference.
It is not necessary for ail positions in a given compound to be uniformly modified, and in fact more than one of the aforementioned modifications can be incorporated in a single compound or even at a single nucleoside within an iRNA. The présent invention also includes iRNA compounds that are chimeric compounds.
“Chimeric” iRNA compounds or “chimeras,” in the context of this invention, are iRNA compounds, preferably dsRNAs, which contain two or more chemically distinct régions, each made up of at least one monomer unit, Le., a nucléotide in the case of a dsRNA compound. These iRNAs typically contain at least one région wherein the RNA is modified so as to confer upon the iRNA increased résistance to nuclease dégradation, increased cellular uptake, or increased binding affînity . for the target nucleic acid. An additional région of the iRNA can serve as a substrate for enzymes capable of cleaving RNa:DNA or RNA:RNA hybrids. By way of example, RNase H is a cellular endonuclease which cleaves the RNa strand of an RNA-.DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of iRNA inhibition of gene expression. Consequently, comparable results can often be obtained with shorter iRNAs when chimeric dsRNAs are used, compared to phosphorothioate deoxy dsRNAs hybridizing to the same target région. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.
In certain instances, the RNA of an iRNA can be modified by a non-ligand group. A number of non-ligand molécules hâve been conjugated to iRNAs in order to enhance the activity, cellular distribution or cellular uptake of the iRNA, and procedures for performing such conjugations are available in the scientifîc literature. Such non-ligand moieties hâve included lipid moieties, such as cholestérol (Kubo, T. et al., Biochem. Biophys. Res. Comm., 2007, 365( 1):54-61 ; Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86:6553), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994,4:1053), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N. Y. Acad. Sci., 1992, 660:306; Manoharan et al., Bioorg. Med. Chem. Let., 1993,3:2765), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992,20:533), an aliphatic chain, e.g., dodecandiol orundecyl residues (SaisonBehmoaras et al., EMBO J., 1991, 10:111; Kabanov et a/., FEBSLett., 1990,259:327; Svinarchuket al., Biochimie, 1993,75:49), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan étal., Tetrahedron Lett., 1995, 36:3651; Shea et al., Nucl. Acids Res., 1990,18:3777), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucléotides, 1995, 14:969), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36:3651), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264:229), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996,277:923). Représentative United States patents that teach the préparation of such RNA conjugales hâve been listed above. Typical conjugation protocols involve the synthesis of an RNAs bearing an aminolinker at one or more positions of the sequence. The amino group is then reacted with the molécule being conjugated using appropriate coupling or activating reagents. The conjugation reaction can be performed either with the RNA still bound to the solid support or following cleavage of the RNA, in solution phase. Purification of the RNA conjugale by HPLC typically affords the pure conjugale.
iii. Delivery of an iRNA of the Invention
The delivery of an iRNA of the invention to a cell e.g., a cell within a subject, such as a human subject infected with HBV can be achieved in a number of different ways. Delivery may also
be performed directly by administering a composition comprising an iRNA, e.g., a dsRNA, to a subject. Alternatively, in vivo delivery may be performed indirectly by administering one or more vectors that encode and direct the expression of the iRNA. These alternatives are discussed further below.
In general, any method of delivering a nucleic acid molécule (in vitro or in vivo) can be adapted for use with an iRNA of the invention (see e.g., Akhtar S. and Julian RL. (1992) Trends Cell. Biol. 2(5):139-144 and WO9402595, which are incorporated herein by reference in their entireties). For in vivo delivery, factors to consider in order to deliver an iRNA molécule include, for example, biological stability of the delivered molécule, prévention of non-specific effects, and accumulation of the delivered molécule in the target tissue. For administering an iRNA systemically for the treatment of a disease, the RNA can be modified or alternatively delivered using a drug delivery system; both methods act to prevent the rapid dégradation of the dsRNA by endo- and exo-nucleases in vivo. Modification of the RNA or the pharmaceutical carrier can also permit targeting of the iRNA composition to the target tissue and avoid undesirable off-target effects. iRNA molécules can be modified by Chemical conjugation to lipophilie groups such as cholestérol to enhance cellular uptake and prevent dégradation. In an alternative embodiment, the iRNA can be delivered using drug delivery Systems such as a nanoparticle, a dendrimer, a polymer, liposomes, or a cationic delivery System. Positively charged cationic delivery Systems facilitate binding of an iRNA molécule (negatively charged) and also enhance interactions at the negatively charged cell membrane to permit efficient uptake of an iRNA by the cell. Cationic lipids, dendrimers, or polymers can either be bound to an iRNA, or induced to form a vesicle or micelle (see e.g., Kim SH., et al (2008) Journal of Controlled Release 129(2): 107-116) that encases an iRNA. The formation of vesicles or micelles further prevents dégradation of the iRNA when administered systemically. Methods for making and administering cationic- iRNA complexes are well within the abilities of one skilled in the art (see e.g., Sorensen, DR., et al (2003) J. Mol. Biol 327:761-766; Verma, UN., et al (2003) Clin. Cancer Res. 9:1291-1300; Arnold, AS et al (2007) J. Hypertens. 25:197-205, which are incorporated herein by reference in their entirety). Some non-limiting examples of drug delivery Systems useful for systemic delivery of iRNAs include DOTAP (Sorensen, DR., et al (2003), supra; Verma, UN., et al (2003), supra), Oligofectamine, solid nucleic acid lipid particles (Zimmermann, TS., et al (2006) Nature 441:111-114), cardiolipin (Chien, PY., et al (2005) Cancer Gene Ther. 12:321-328; Pal, A., et al (2005) Int J. Oncol. 26:1087-1091), polyethyleneimine (Bonnet ME., et al (2008) Pharm. Res. Aug 16 Epub ahead of print; Aigner, A. (2006) J. Biomed. Biotechnol. 71659), Arg-Gly-Asp (RGD) peptides (Liu, S. (2006) Mol. Pharm. 3:472-487), and polyamidoamines (Tomalia, DA., et al (2007) Biochem. Soc. Trans. 35:61-67; Yoo, H., et al (1999) Pharm. Res. 16:1799-1804). In some embodiments, an iRNA forms a complex with cyclodextrin for systemic administration. Methods for administration and pharmaceutical compositions of iRNAs and cyclodextrins can be found in US Patent No. 7,427,605, which is herein incorporated by reference in its entirety. In certain embodiments, the iRNA agents can be administered with amphipathic peptides to facilitate pH-
dépendent endosomal escape (see, e.g., Bartz et al., 2011. Biochem. J. 435:475-87, incorporated herein by reference)
1. Vector encoded iRNAs for use in the Invention iRNA targeting an HBV gene can be expressed from transcription units inserted into DNA or
RNA vectors (see, e.g., Couture, A, et al., TIG. (1996), 12:5-10; Skillem, A., et al., WO 00/22113, WO 00/22114, and US Patent No. 6,054,299). Exemplary expression vectors for expression of shRNA targeted to HBV are provided in Michler et al., 2016 which discloses adeno-associated virus (AAV) 8 vectors for delivery included (i) embedded the shRNA in an artifîcial mi(cro)RNA under a 10 liver-specific promoter, (ii) co-expressed Argonaute-2, a rate limiting cellular factor whose saturation with excess RNAi triggers can be toxic; or (iii) co-delivered a decoy (“TuD”) directed against the shRNA sense strand to curb off-target gene régulation. The plasmids expressing shRNAs shHBV4 to 7 that were used in the cell culture studies were cloned by direct insertion of the respective shRNAencoding oligonucleotides into a self-complementary AAV vector plasmid previously reported by 15 Grimm et al, 2006 (Nature 441: 537 - 541), containing an H1 promoter followed by two Bbsl sites for oligonucleotide insertion as well as an RSV promoter. Such constructs can also be used for the expression of vaccine antigens if appropriately sized for the expression vector.
Expression can be transient (on the order of days to weeks) or sustained (weeks to months, or longer), depending upon the spécifie construct used and the target tissue or cell type. These transgenes can be introduced as a linear construct, a circular plasmid, or a viral vector, which can be an integrating or non-integrating vector. The transgene can also be constructed to permit it to be inherited as an extrachromosomal plasmid (Gassmann, et al., Proc. Natl. Acad. Sci. USA (1995) 92:1292).
The individual strand or strands of an iRNA can be transcribed from a promoter on an 25 expression vector. Where two separate strands are to be expressed to generate, for example, a dsRNA, two separate expression vectors can be co-introduced (e.g., by transfection or infection) into a target cell. Alternatively each individual strand of a dsRNA can be transcribed by promoters both of which are located on the same expression plasmid. In one embodiment, a dsRNA is expressed as inverted repeat polynucleotides joined by a linker polynucleotide sequence such that the dsRNA has a 30 stem and loop structure.
iRNA expression vectors are generally DNA plasmids or viral vectors. Expression vectors compatible with eukaryotic cells, preferably those compatible with vertebrate cells, can be used to produce recombinant constructs for the expression of an iRNA as described herein. Eukaryotic cell expression vectors are well known in the art and are available from a number of commercial sources. 35 Typically, such vectors are provided containing convenient restriction sites for insertion of the desired nucleic acid segment. Delivery of iRNA expressing vectors can be systemic, such as by subeutaneous, intravenous, or intramuscular administration. Such vectors can also be used for expression of viral antigens from nucleic acid-based vaccines.
Viral vector Systems which can be utilized with the methods and compositions described herein include, but are not limited to, (a) adenovirus vectors; (b) retrovirus vectors, including but not limited to lentiviral vectors, moloney murine leukemia virus, etc.·, (c) adeno-associated virus vectors; (d) herpes simplex virus vectors; (e) SV 40 vectors; (f) polyoma virus vectors; (g) papilloma virus vectors; (h) picomavirus vectors; (i) pox virus vectors such as an orthopox, e.g., vaccinia virus vectors including modified vaccinia virus Ankara vector or avipox, e.g. canary pox or fowl pox; and (j) a helper-dependent or gutless adenovirus. Replication-defective viruses can also be advantageous. Different vectors will or will not become incorporated into the cells’ genome. The constructs can include viral sequences for transfection, if desired. Alternatively, the construct can be incorporated into vectors capable of episomal réplication, e.g. EPV and EBV vectors. Constructs for the recombinant expression of an iRNA or HBV antigen will generally require regulatory éléments, e.g., promoters, enhancers, etc., to ensure the expression of the iRNA in target cells. Other aspects to consider for vectors and constructs are further described below.
Such constructs and vectors can also be used for the expression of vaccine antigens if appropriately sized for the expression vector. Such limitations are well understood by those of skill in the art.
B. Therapeutic HBV Vaccines For Use in the Mehods of the Invention
Therapeutic HBV vaccines for use in the regimens and methods of the invention can be a peptide vaccine, a DNA vaccine including a vector-based vaccine, or cell-based vaccine that induces an immune response, preferably an effector T cell induced response, against one or more HBV proteins. Preferably the vaccine is a multi-epitope vaccine that is cross-reactive with multiple HBV serotypes, preferably ail HBV serotypes.
A therapeutic vaccine is designed to activate the patient's immune System to recognize and control or eliminate an already established pathogen infection. This is clearly distinct from a prophylactic vaccination which is designed to promote rapid antibody-mediated neutralization of an invading pathogen. Control and élimination of persistent viruses such as hepatitis, herpes, or papilloma viruses requires multi-specific and poly-functional effector T cell responses. These T cell responses are ideally directed against continuously expressed viral antigens to keep the pathogen in check. Therapeutic vaccines are under development for a number of chronic infections. Hepatitis B virus infection is a candidate for treatment by therapeutic vaccination since a spontaneous, inununemediated recovery of chronic hepatitis B and an élimination of the virus has been observed in very rare cases.
Robust T cell responses seem to be essential to achieve HBV cure. While HBV-specific CD4+ and CD8+ T cell responses are readily détectable in patients resolving HBV infection, HBVspecific T cells are scarce and functionally impaired in chronic hepatitis B most likely due to high amounts of circulating viral HBeAg and HBsAg. T cells eliminate HBV infected cells by their cytotoxic activity but also control HBV gene expression and réplication in a non-cytolytic fashion.
To overcome immune tolérance in chronic hepatitis B different approaches hâve been investigated in preclinical models using DNA or peptide vaccines, or vector- or cell-based vaccines to induce an effector T cell response. Multi-epitope therapeutic vaccine candidates that cover sufficient different HBV génotypes and most frequent HLA types hâve been developed. Although proper peptide présentation was demonstrated, immunogenicity was limited and the approach was not translated into the clinics. A non-exhaustive list is provided in the table below.
Therapeutic HBV Vaccine Tables
Vaccine Name Proteins/ coding séquences Vaccine type/ Composition Results available Sponsor Development Stage Clinical Trial Reference No. References (the entire contents of each of which are incorporated herein by reference)
HB-110 HBsAg,, HBeAg, human IL-12 3 Plasmid based DNA vaccine Study completed, results not reported Genexine Phase I NCT01813487 NCT01641536 NCT00513968 Kim et al., 2008. Exp Mol Med. 40:669-676
HB-100 pGXlO S +pGX10 S1/S2/X +pGX10 core +pGX10Pol +pGX10hIL12N222L 5 Plasmid based DNA vaccine - 4 antigens + human IL-12 Yang et al., 2006. Gene Therapy. 13:1110-1117
ppdpSC18 DNA vaccine adjuvanted with particle mediated epidermal delivery Study completed, results not reported PowderMed Phase I NCT00277576
INO-1800 HbsAg, HBeAg DNA plasmid Recruiting Inovio Pharmaceuticals Phase I NCT02431312
HB02 VAC- ADN HB preS/S pCMV-S2.S DNA vaccine; CMV promoter, plasmid vector Well tolerated; No change in relapse rate in HBV treated patients or decrease in virological breakthrough ANRS Phase I/II NCT00536627 Mancini - Bourgine et al., 2006. Vaccine 24:44824489
CVI-HBV-002 HbsAg DNA+ L-pampo Recruiting CHA Vaccine Institute Co., Ltd. Phase I/II NCT02693652
Theravax (DV601) HBsAg, HBeAg Protein + adjuvant Well tolerated; anti-viral response observed in ail patients Dynavax Technologies Corp. Phase Ib NCTO1023230
HepTcell™ IC31® adjuvanted peptide Recruiting Altimmune, Inc. Phase I NCT02496897 US 20130330382 US 20120276138 US 20150216967
HBsAg/HBcAg HBsAg HBeAg protein Research Li et al., 2015, Vaccine. 33:4247-4254
GS-4774 Fusion protein HBsAg, HBeAg, HBxAg Protein + Tamogen T cell stimulator Phase Π naïve group ongoing; no signifïcant viral decrease in treatment- Gilead Phase II NCTO 1943799 NCT01779505 NCT02174276 Gaggareta/,,2014. Vaccine. 32:4925-4931.
expérience patients
εΡΑ-44 Multi-peptide vaccine Some séroconversion observed in ail groups, no statistical analysis Chongqing Jaichen Biotechnology, Ltd. Phase II NCT00869778 NCT02862106
ΑΒΧ 203 HBsAg, HBcAg HBsAg, HBcAg Ongoing ABIVAX S.A. Phase ΙΙ/ΙΠ NCT02249988
pSG2.HBs/ MVA.HBs Protein primeviral vector boost Well tolerated, but did not control HBV infection Oxxon Therapeutics Phase lia ISRCTN 67270384 Cavenaugh et al., 2011. PLoS ONE 6: el4626.
HBsAg, HBcAg Adjuvanted protein primeviral vector boost Research Backes, 2016, Vaccine; WO2017121791
Existing prophylactic vaccines hâve been used to restore HBV-specific immunity in chronically infected patients, but hâve failed to provide a functional cure. These subviral particlebased vaccines were able to reduce HBV réplication in animal models of chronic hepadnaviral infection, but hâve not been successfiil in patients with chronic hepatitis B. An antigen-antibody (HBsAg-HBIG) immunogenic complex therapeutic vaccine candidate with alum as adjuvant first showed promising results in a double-blind, placebo controlled, phase Hb clinical trial, but results of a phase ΙΠ clinical trial including 450 patients were disappointing. This is most likely due to the fact that subviral particle vaccines with alum-based adjuvants are designed as prophylactic vaccines and preferentially induce antibodies but not cytotoxic T cell responses that would be required for therapeutic efficacy.
Alternatively, DNA vaccines encoding HBV envelope proteins were designed to induce HBV-specific T cells but also had limited success. Since DNA-based vaccines hardly induce antibody responses, they failed to achieve HBeAg or HBsAg séroconversion. An alternative DNA prime, poxvirus-boost vaccine encompassing the HBV preS/S région encoding for the HBV envelope 15 proteins showed promising results in chimpanzees, but also failed in a clinical phase lia trial neither inducing sustained T cell responses nor reducing viremia in chronic HBV carriers. They may hâve failed to induce T cell help or broad enough, multi-specific immune responses.
Any vaccines known in the art can be used in the methods and regimens provided herein. Preferred embodiments include the prime-boost vaccination scheme with protein antigens administered twice and a nucleic acid vaccine administered once as provided in the Examples and provided in PCT Publication No. WO 2017/121791 (the entire contents of which are incorporated herein by reference). As discussed above, the sequence of the protein antigen in the vaccine and the amino acid sequence encoded by nucleic acid-based vaccine need not be identical. They simply must share at least one epitope, preferably multiple epitopes, so that the sequential administration of the vaccines has the desired prime-boost effect. Further, as discussed herein, in preferred embodiments, the treatment regimen provided herein would provide a treatment regimen effective across multiple, if not ali, HBV serotypes. Therefore, it is understood that the antigen delivered to the subject may not hâve antigen sequences identical to the antigens expressed by the HBV virus that infected the subject.
It is known in the art that some portions of HBV antigens are the main targets of antibodies 30 generated during the initial immune response to infection with HBV known as déterminants. For example the HBsAg includes the a déterminant epitope that is located at amino acids 124 to 147 within the major hydrophilic région (MHR, amino acids 100 to 169) of the 226 amino acid S gene (SEQ ID NO: 8 or 22). This a déterminant is one of the main targets of anti-HBs antibodies during the course of the initial immune response in acute hepatitis B. In certain embodiments, an immunogenic fragment of HBsAg comprises compared to the full length protein at least amino acids 99 to 168 corresponding to the amino acid positons of the small envelope protein (SEQ ID NO: 23) (see, e.g., Lada et al., J. Virol.(2006) 80:2968-2975, the entire contents of which are incorporated herein by reference).
Similarly, déterminants hâve been identified in HBcAg (see, e.g., Salfeld et al., J. Virol. (1989) 63:798-808, the entire contents of which are incorporated herein by reference). The fiill-length core protein is 183 amino acids in length and consiste of an assembly domain (amino acids 1 to 149) and a nucleic acid-binding domain (amino acids 150 to 183). Three distinct major déterminants hâve been characterized. The single conformational déterminant responsible for HBc antigenicity in the assembled core (HBc) and a linear HBe-related déterminant (HBel) were both mapped to an overlapping hydrophilic sequence around amino acid 80; a second HBe déterminant (HBe2) was assigned to a location in the vicinity of amino acid 138 but found to require for its antigenicity the intramolecular participation of the extended sequence between amino acids 10 and 140. Typically, 10 such an immunogenic fragment comprises, compared to the full length core protein, at least amino acids 18 to 143 corresponding to the sequence positions set forth in SEQID NO: 24. Analogous sequences can be identified in SEQ ID NO: 10.
In preferred embodiments, the vaccines include an amino acid sequence or encode an amino acid sequence that includes at least one déterminant of HBsAg or HBcAg. Specifically, in certain embodiments, a vaccine targeted to HBsAg includes at least the amino acid sequence of amino acids 127 to 147 of HBsAg, e.g., includes at least amino acids 99 to 168 of the amino acid sequence of the small envelope protein (SEQ ID NO: 23). In certain embodiments, a vaccine targeted to a hydrophilic sequence at least around amino acid 80 of HBcAg or an amino acid sequence at least around amino acid 138, e.g., at least a 40 amino acid portion, at least a 50 amino acid portion, at least a 60 amino acid portion, at least a 70 amino acid portion, at least an 80 amino acid portion, at least a 90 amino acid portion, or at least a 100 amino acid portion of SEQ ID NO: 43 including amino acid 80 or amino acid 138, or a coding sequence therefor. In preferred embodiments, the antigen amino sequence of the antigen targeted to HBcAg includes at least 20 amino acids N-terminal and C-terminal to amino acid 80 or 138 of SEQ ID NO: 24. In certain embodiments, a vaccine targeted to HBcAg includes at least the amino acid sequence of amino acids 10 to 140 or 18 to 143 of HBsAg.
In certain embodiments, the vaccine may comprise the entire amino acid sequence or encode the entire amino acid sequence of any one or more of SEQ ID NO: 22,23, or 24.
. It is understood that there are multiple serotypes of HBV with different nucleic acid sequences that encode different amino acid sequences. Therefore, it is understood that the amino acid 30 sequence of a protein-based vaccine or the amino acid sequence encoded by a nucleic acid-based vaccine may not be 100% identical to the sequences provided in the SEQ ID NOs. In certain embodiments of the invention, the the amino acid sequence of a protein-based vaccine or the amino acid sequence encoded by a nucleic acid-based vaccine is at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at 35 least 96% identical, at least 97% identical, or at least 98% identical to the portion of SEQ ID NO: 22, 23, or 24. Additional exemplary HBsAg and HBcAg amino acid sequenences are provided in the sequence listing. Alignment methods to identify appropriate sequences corresponding to the HBsAg and HBcAg déterminants in the sequences indicated above are known in the art.
The vaccine preferably comprises MVA viruses in a concentration range of 104 to 10’ tissueculture infections dose (TCIDjso/ml, preferably in a concentration range of 105 to 5xl08 TCIDso/ml, more preferably in a concentration range of 106 to 108 TCIDso/ml, and most preferably in a concentration range of 107 to 108 TCIDjo/ml.
A preferred vaccination dose for humans comprises 106 to 109 TCIDso, most preferably a dose of 106 TCIDso or 107 TCIDso or 108 TCIDso.
The preferred methods of the invention include administration of both a protein-based vaccine and a nucleic acid-based vaccine. However, other methods include administration of only protein antigens. Less preferred embodiments include administration of only nucleic acids encoding antigens.
i. Adjuvants
As used herein “adjuvant” is understood as an agent that promotes (e.g., enhances, accelerates, or prolongs) an immune response to an antigen with which it is administered to elicit long-term protective immunity. No substantial immune response is directed at the adjuvant itself.
Adjuvants include, but are not limited to, pathogen components, particulate adjuvants, and combination adjuvants (see, e.g., www.niaid.nih.gov/research/vaccine-adjuvants-types). Pathogen components (e.g., monophosphoryl lipid A (MPL), poly(I:C), CpG DNA, émulsions such as poly[di(sodiumcarboxylatoethylphenoxy)phosphazene] (PCEP)) can help trigger early non-specifïc, or innate, immune responses to vaccines by targeting various receptors inside or on the surface of innate immune cells. The innate immune system influences adaptive immune responses, which provide long-lasting protection against the pathogen that the vaccine targets. Particulate adjuvants (e.g., alum, virosomes, cytokines, e.g., IL-12) form very small particles that can stimulate the immune system and also may enhance delivery of antigen to immune cells. Combination adjuvants (e.g., AS02, AS03 and AS04 (GSK); MF59 (Novartis); and IC31® (Altimmune) elicit multiple protective immune responses. Adjuvants that hâve a modest effect when used alone may induce a more potent immune response when used together. In certain embodiments, preferred adjuvants include c-diAMP, c-di-GMP, c-di-CMP, PolyICLC, CpG, ISCOMATRIX®, AS02, AS03, AS04, or a RIG-I ligand such as 5’ 3P-RNA. In certain embodiments, a viral capsid, with or without a nucleic acid expressing an HBV antigen can be used as an adjuvant. For example, a vaccine that preferentially stimulâtes T cells such as an MVA-only or a DNA prime, MVA boost or an adenovirus vector primeMVA boost can be used in the methods of the invention.
In preferred embodiments of the invention, adjuvants for use in the invention promote a humoral and a cellular immune response as discussed above. In certain embodiments, adjuvants provide a balanced Thl/Th2 response.
ii. Non-adjuvant immune stimulators and additional agents
Methods of the invention can further include administration of additional agents used in the treatment of HBV or to stimulate an immune response. Such agents can include an immune
d.
stimulator (e.g., pegylated interferon alfa 2a (PEG-IFN-a2a), Interferon alfa-2b, a recombinant human interleukin-7, and aToll-like receptor 3, 7, 8, or 9 (TLR3, TLR7, TLR8, or TLR9) agonist), a viral entry inhibitor (e.g., Myrcludex), an oligonucleotide that inhibits the sécrétion or release of HBsAg (e.g., REP 9AC), a capsid inhibitor (e.g., Bay41-4109 and NVR-1221), a cccDNA inhibitor (e.g.,
IHVR-25), a Rig-I-ligand, a STING agonist, an antibody based immune therapy against HBV (mono-, bi-, or trispecific antibody against HBV), or an immune checkpoint regulator. Such agents are known in the art.
C. Nucléotide and Nucleoside Analogs For Use in the Methods of the Invention
Nucléotide and nucleoside analogs are considered to be the standard of care for HBV infection as they are generally considered safe and inexpensive. However, nucléotide and nucleoside analogs cannot cure HBV infection, may cause the development of résistance, and must be taken indefmitely. Nucléotide analog and nucleoside analogs include, but are not limited to, Tenofovir disoproxil fumarate (TDF), Tenofovir alafenamide, Lamivudine, Adefovir dipivoxil, Entecavir (ETV), Telbivudine, AGX-1009, emtricitabine, clevudine, ritonavir, dipivoxil, lobucavir, famvir, FTC, N-Acetyl-Cysteine (NAC), PC 1323, theradigm-HBV, thymosin-alpha, ganciclovir, Besifovir (ANA-380/LB-80380), and Tenofvir-Exalidex (TXL/CMX157) . In certain embodiments, the nucelot(s)ide analog is Entecavir (ETV) or Tenofovir or a dérivative thereof. In certain embodiments, the nucleot(s)ide analog is not Lamivudine. Nucleot(s)ide analogs are commercially available from a number of sources and are used in the methods provided herein according to their label indication (e.g., typically orally administered at a spécifie dose) or as determined by a skilled practitioner in the treatment of HBV.
III. Antisense Oligonucleotides Targeting HBV
The présent invention includes the use of iRNAs which promote cleavage of at least one HBV transcript, and preferably three or four HBV transcripts. Antisense oligonucleotides can similarly be used to promote cleavage of at least one HBV transcript, preferably three or four HBV transcripts, in the methods of the invention provided here. Exemplary antisense oligonucleotides targeted to HBV are provided, for example, in U.S. Patent Publication Nos. 2013/0035366,2012/0207709, and
2004/0127446, the contents of each of which is incorporated by reference herein in its entirety.
It is understood by those of skill in the art that conjugales, linkers, and formulations for the delivery of siRNAs as provided above can be used for the formulation and delivery of antisense oligonucleotide therapeutic agents to subjects.
IV. Pharmaceutical Compositions of the Invention
The présent invention also includes pharmaceutical compositions and formulations which include the iRNAs or vaccines for use in the invention. It is understood that approved therapeutic agents are formulated and administered by the route indicated on their package instructions.
In some embodiments, provided herein are pharmaceutical compositions containing an iRNA or a vaccine, as described herein, and a pharmaceutically acceptable carrier. The pharmaceutical compositions containing the iRNA or vaccine are usefiil for treating subject with an HBV infection. Such pharmaceutical compositions are formulated based on the mode of delivery, e.g., for systemic administration via parentéral delivery, e.g., by subcutaneous (SC), intramuscular (IM), or intravenous (IV) delivery.
The pharmaceutical RNAi compositions for use in the invention may be administered in dosages sufficient to significantly reduce the level of at least one HBV transcript. In general, a suitable dose of an iRNA of the invention will be in the range of about 0.001 to about 200.0 milligrams per kilogram body weight of the récipient per day, generally in the range of about 1 to 50 mg per kilogram body weight per day. Typically, a suitable dose of an iRNA of the invention will be in the range of about 0.1 mg/kg to about 5.0 mg/kg, preferably about 0.3 mg/kg and about 3.0 mg/kg. A repeat-dose regimen may include administration of a therapeutic amount of iRNA on a regular basis, such as every other week or once a year. In certain embodiments, the iRNA is administered about once per month to about once per quarter (i.e., about once every three months). In preferred embodiments, the RNAi agent is administered subcutaneously.
Formulation and dosing of the vaccine will dépend on the nature of the vaccine administered. In a protein prime-expression vector boost vaccination strategy, the protein-based priming vaccines are administered about 2,3, or 4 weeks apart with the expression vector vaccine boost being administered about 2,3, or 4 weeks after the second protein-based vaccine dose. In certain embodiments, it is about two weeks between the first and second doses of the protein-based vaccine. In certain embodiments, it is about two weeks between the second dose of the protein based vaccine and the DNA expression vector vaccine boost. In certain embodiments, the prime and boost vaccinations are administered by routes independently selected from intramuscularly, intradermally, 25 or subcutaneously.
The pharmaceutical nucleic acid-based vaccines for use in the invention may be administered in dosages sufficient to promote an immune response, as either a prime agent or a boost agent. The amount of nucleic acid-based vaccine to be administered will dépend, for example, on the design of the vaccine. As the regimens provided herein can include the use of existing nucleic acid-based vaccines, knowledge regarding appropriate dosages based on therapeutic efficacy and safety should be based on the spécifie agent used.
The pharmaceutical protein-based vaccines for use in the invention may be administered in dosages sufficient to promote an immune response, as either a prime or a boost agent. The amount of protein-based vaccine to be administered will dépend, for example, on the adjuvant used. Protein35 based vaccines can be dosed, for example, at about 5-100 mg/kg/dose, about 10-50 mg/kg/dose, or about 20-40 mg/kg/dose. As the regimens provided herein can include the use of existing proteinbased vaccines, knowledge regarding appropriate dosages based on therapeutic efficacy and safety should be based on the spécifie agent used.
After an initial treatment regimen, the treatments can be administered on a less frequent basis. In preferred embodiments, the treatment regimens and methods provided herein resuit in a functional cure allowing for discontinuation of treatment after completion of the regimen or after diagnostic criteria indicate a functional cure, e.g., decreased HBsAg levels preferably to below the level of détection of the methods provided herein and a détectable immune response to HBsAg.
The skilled artisan will appreciate that certain factors can influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health or âge of the subject, and other diseases présent. Moreover, treatment of a subject with a therapeutically effective amount of a composition can include 10 a single treatment or a sériés of treatments. Estimâtes of effective dosages and in vivo half-lives for the individual therapeutic agent used in the methods and regimens invention can be made using conventional méthodologies or on the basis of in vivo testing using an appropriate animal model, as described elsewhere herein and known in the art.
A. iRNA Formulations Comprising Membranous Molecular Assemblies
An iRNA for use in the compositions and methods of the invention can be formulated for delivery in a membranous molecular assembly, e.g., a liposome or a micelle. As used herein, the term “liposome” refers to a vesicle composed of amphiphilic lipids arranged in at least one bilayer, e.g., one bilayer or a plurality of bilayers. Liposomes include unilamellar and multilamellar vesicles that 20 hâve a membrane formed from a lipophilie material and an aqueous interior. The aqueous portion contains the iRNA composition. The lipophilie material isolâtes the aqueous interior from an aqueous exterior, which typically does not include the iRNA composition, although in some examples, it may. Liposomes are useful for the transfer and delivery of active ingrédients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied 25 to a tissue, the liposomal bilayer fuses with bilayer of the cellular membranes. As the merging of the liposome and cell progresses, the internai aqueous contents that include the iRNA are delivered into the cell where the iRNA can specifically bind to a target RNA and can médiate iRNA. In some cases the liposomes are also specifically targeted, e.g., to direct the iRNA to particular cell types.
A liposome containing an iRNA agent can be prepared by a variety of methods. In one 30 example, the lipid component of a liposome is dissolved in a detergent so that micelles are formed with the lipid component. For example, the lipid component can be an amphipathic cationic lipid or lipid conjugate. The detergent can hâve a high critical micelle concentration and may be nonionic. Exemplary détergents include cholate, CHAPS, octylglucoside, deoxycholate, and lauroyl sarcosine. The iRNA agent préparation is then added to the micelles that include the lipid component. The cationic groups on the lipid interact with the iRNA agent and condense around the iRNA agent to form a liposome. After condensation, the detergent is removed, e.g., by dialysis, to yield a liposomal préparation of the iRNA agent.
If necessary a carrier compound that assists in condensation can be added during the condensation reaction, e.g., by controlled addition. For example, the carrier compound can be a polymer other than a nucleic acid (e.g., spermine or spermidine). pH can also adjusted to favor condensation.
Methods for producing stable polynucleotide delivery vehicles, which incorporate a polynucleotide/cationic lipid complex as structural components of the delivery vehicle, are further described in, e.g., WO 9637194, the entire contents of which are incorporated herein by reference. Liposome formation can also include one or more aspects of exemplary methods described in Felgner, P. L. étal., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987; US Patent No. 4,897,355; US Patent No.
5,171,678; Bangham, et al. M. Mol. Biol. 23:238, 1965; Oison, et al. Biochim. Biophys. Acta 557:9,
1979; Szoka, et al. Proc. Natl. Acad. Sci. USA 75: 4194,1978; Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984; Kim, et al. Biochim. Biophys. Acta 728:339,1983; and Fukunaga, et al. Endocrinol. 115:757,1984. Commonly used techniques for preparing lipid aggregates of appropriate size for use as delivery vehicles include sonication and freeze-thaw plus extrusion (see, e.g., Mayer, et al.
Biochim. Biophys. Acta 858:161, 1986). Microfluidization can be used when consistently small (50 to 200 nm) and relatively uniform aggregates are desired (Mayhew, et al. Biochim. Biophys. Acta 775:169,1984). These methods are readily adapted to packaging iRNA agent préparations into liposomes.
Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes 20 which interact with the negatively charged nucleic acid molécules to form a stable complex. The positively charged nucleic acid/liposome complex binds to the negatively charged cell surface and is intemalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147,980-985).
Liposomes which are pH-sensitive or negatively-charged, entrap nucleic acids rather than complex with it. Since both the nucleic acid and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some nucleic acid is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes hâve been used to deliver nucleic acids encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of ControlledRelease, 1992, 19,269-274).
One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic 35 liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC and egg PC. Another type is formed from mixtures of phospholipid or phosphatidylcholine or cholestérol.
Examples of other methods to introduce liposomes into cells in vitro and in vivo include US Patent Nos. 5,283,185 and 5,171,678; WO 94/00569; WO 93/24640; WO 91/16024; Felgner, J. Biol. Chem. 269:2550, 1994; Nabel, Proc. Natl. Acad. Sci.USA 90:11307, 1993; Nabel, Human Gene Ther. 3:649, 1992; Gershon, Biochem. 32:7143,1993; and Strauss EMBOJ. 11:417, 1992.
Non-ionic liposomal Systems hâve also been examined to détermine their utility in the delivery of drugs to the skin, in particular Systems comprising non-ionic surfactant and cholestérol. Non-ionic liposomal formulations comprising Novasome™ I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome™ Π (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the 10 dermis of mouse skin. Results indicated that such non-ionic liposomal Systems were effective in facilitating the déposition of cyclosporine A into different layers of the skin (Hu et al. S.T.P.Pharma. Sci., 1994,4(6) 466).
Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, resuit 15 in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids. Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside Gmi, or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. While not wishing to be bound by any particular theory, it is thought in the art that, at least for sterically stabilized liposomes containing gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced circulation half-life of these sterically stabilized liposomes dérivés from a reduced uptake into cells of the réticuloendothélial System (RES) (Allen et al., FEBS Letters, 1987,223,42; Wu et al., Cancer Research, 1993, 53, 3765).
Varions liposomes comprising one or more glycolipids are known in the art. Papahadjopoulos 25 et al. (Ann. N.Y. Acad. Sci., 1987, 507, 64) reported the ability of monosialoganglioside Gmi, galactocerebroside sulfate and phosphatidylinositol to improve blood half-lives of liposomes. These findings were expounded upon by Gabizon et al. (Proc. Natl. Acad. Sci. USA, 1988, 85, 6949). US Patent No. 4,837,028 and WO 88/04924, both to Allen et al., disclose liposomes comprising (1) sphingomyelin and (2) the ganglioside Gmi or a galactocerebroside sulfate ester. US Patent No.
5,543,152 discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sndimyristoylphosphatidylcholine are disclosed in WO 9713499 (Lim et al).
Cationic liposomes possess the advantage of being able to fuse to the cell membrane. Noncationic liposomes, although not able to fuse as efficiently with the plasma membrane, are taken up by macrophages in vivo and can be used to deliver iRNA agents to macrophages.
Further advantages of liposomes include: liposomes obtained from naturel phospholipids are biocompatible and biodégradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated iRNA agents in their internai compartments from metabolism and dégradation (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and
Banker (Eds.), 1988, volume 1, p. 245). Important considérations in the préparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.
A positively charged synthetic cationic lipid, N-[l-(2,3-dioleyloxy)propyl]-N,N,Ntrimethylammonium chloride (DOTMA) can be used to form small liposomes that interact spontaneously with nucleic acid to form lipid-nucleic acid complexes which are capable of fiising with the negatively charged lipids of the cell membranes of tissue culture cells, resulting in delivery of iRNA agent (see, e.g., Felgner, P. L. et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987 and US Patent No. 4,897,355 for a description of DOTMA and its use with DNA).
A DOTMA analogue, l,2-bis(oleoyloxy)-3-(trimethylammonia)propane (DOTAP) can be used in combination with a phospholipid to form DNA-complexing vesicles. Lipofectin™ Bethesda Research Laboratories, Gaithersburg, Md.) is an effective agent for the delivery of highly anionic nucleic acids into living tissue culture cells that comprise positively charged DOTMA liposomes which interact spontaneously with negatively charged polynucleotides to form complexes. When enough positively charged liposomes are used, the net charge on the resulting complexes is also positive. Positively charged complexes prepared in this way spontaneously attach to negatively charged cell surfaces, fuse with the plasma membrane, and efficiently deliver fiinctional nucleic acids into, for example, tissue culture cells. Another commercially available cationic lipid, 1,2bis(oleoyloxy)-3,3-(trimethylammonia)propane (“DOTAP”) (Boehringer Mannheim, Indianapolis, Indiana) differs from DOTMA in that the oleoyl moieties are linked by ester, rather than ether linkages.
Other reported cationic lipid compounds include those that hâve been conjugated to a variety of moieties including, for example, carboxyspermine which has been conjugated to one of two types of lipids and includes compounds such as 5-carboxyspermylglycine dioctaoleoylamide (“DOGS”) (Transfectam™, Promega, Madison, Wisconsin) and dipalmitoylphosphatidylethanolamine 525 carboxyspermyl-amide (“DPPES”) (see, e.g., US Patent No. 5,171,678).
Another cationic lipid conjugate includes derivatization of the lipid with cholestérol (“DCChol”) which has been formulated into liposomes in combination with DOPE (See, Gao, X. and Huang, L., Biochim. Biophys. Res. Commun. 179:280, 1991). Lipopolylysine, made by conjugating polylysine to DOPE, has been reported to be effective for transfection in the presence of sérum (Zhou,
X. et al., Biochim. Biophys. Acta 1065:8, 1991). For certain cell lines, these liposomes containing conjugated cationic lipids, are said to exhibit lower toxicity and provide more efficient transfection than the DOTMA-containing compositions. Other commercially available cationic lipid products include DMRIE and DMRIE-HP (Vical, La Jolla, California) and Lipofectamine (DOSPA) (Life Technology, Inc., Gaithersburg, Maryland). Other cationic lipids suitable for the delivery of oligonucleotides are described in WO 98/39359 and WO 96/37194.
Liposomal formulations are particularly suited for topical administration. Liposomes présent several advantages over other formulations. Such advantages include reduced side effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at
C<
the desired target, and the ability to administer iRNA agent into the skin. In some implémentations, liposomes are used for delivering iRNA agent to epidermal cells and also to enhance the pénétration of iRNA agent into dermal tissues, e.g., into skin. For example, the liposomes can be applied topically. Topical delivery of drugs formulated as liposomes to the skin has been documented (see, 5 e.g., Weiner et al., Journal ofDrug Targeting, 1992, vol. 2,405-410 and du Plessis et al., Antiviral
Research, 18, 1992,259-265; Mannino, R. J. and Fould-Fogerite, S., Biotechniques 6:682-690, 1988; Itam, T. et al. Gene 56:267-276.1987; Nicolau, C. et al. Meth. Enz. 149:157-176, 1987; Straubinger, R. M. and Papahadjopoulos, D. Meth. Enz. 101:512-527, 1983; Wang, C. Y. and Huang, L., Proc. Natl. Acad. Sci. USA 84:7851-7855,1987).
Liposomes that include iRNA can be made highly déformable. Such deformability can enable the liposomes to penetrate through pore that are smaller than the average radius of the liposome. For example, transfersomes are a type of déformable liposomes. Transferosomes can be made by adding surface edge activators, usually surfactants, to a standard liposomal composition. Transfersomes that include iRNA agent can be delivered, for example, subcutaneously by infection in order to deliver iRNA agent to kératinocytes in the skin. In order to cross intact mammalian skin, lipid vesicles must pass through a sériés of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. In addition, due to the lipid properties, these transferosomes can be self-optimizing (adaptive to the shape of pores, e.g., in the skin), self-repairing, and can frequently reach their targets without fragmenting, and often self-loading.
Other formulations amenable to the présent invention are described in WO 2008042973.
Surfactants find wide application in formulations such as émulsions (including microemulsions) and liposomes. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group (also known as the head) provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in “Pharmaceutical Dosage Forms”, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).
If the surfactant molécule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.
If the surfactant molécule carnes a négative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.
If the surfactant molécule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quatemary ammonium salts and 5 ethoxylated amines. The quatemary ammonium salts are the most used members of this class.
If the surfactant molécule has the ability to carry either a positive or négative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid dérivatives, substituted alkylamides, N-alkylbetaines and phosphatides.
The use of surfactants in drug products, formulations and in émulsions has been reviewed 10 (Rieger, in “Pharmaceutical Dosage Forms”, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).
The iRNA for use in the methods of the invention can also be provided as micellar formulations. “Micelles” are defined herein as a particular type of molecular assembly in which amphipathic molécules are arranged in a spherical structure such that ail the hydrophobie portions of the molécules are directed inward, leaving the hydrophilic portions in contact with the surrounding 15 aqueous phase. The converse arrangement exists if the environment is hydrophobie.
B. Lipidparticles iRNAs, e.g., dsRNAs of in the invention may be fully encapsulated in a lipid formulation, e.g., a LNP, or other nucleic acid-lipid particle. Expression vectors or RNAs containing coding 20 sequences for viral antigens under the control of an appropriate promoter can be formulated in lipid particles for delivery.
As used herein, the term LNP refers to a stable nucleic acid-lipid particle. LNPs typically contain a cationic lipid, a non-cationic lipid, and a lipid that prevents aggregation of the particle (e.g., a PEG-lipid conjugale). LNPs are extremely usefiil for systemic applications, as they exhibit extended 25 circulation lifetimes following intravenous (i.v.) injection and accumulate at distal sites (e.g., sites physically separated from the administration site). LNPs include pSPLP, which include an encapsulated condensing agent-nucleic acid complex as set forth in WO 0003683. The particles of the présent invention typically hâve a mean diameter of about 50 nm to about 150 nm, more typically about 60 nm to about 130 nm, more typically about 70 nm to about 110 nm, most typically about 70 30 nm to about 90 nm, and are substantially nontoxic. In addition, the nucleic acids when présent in the nucleic acid- lipid particles of the présent invention are résistant in aqueous solution to dégradation with a nuclease. Nucleic acid-lipid particles and their method of préparation are disclosed in, e.g., US Patent Nos. 5,976,567; 5,981,501; 6,534,484; 6,586,410; and 6,815,432; US20100324120 and WO 9640964.
In some embodiments, the lipid to drug ratio (mass/mass ratio) (e.g., lipid to dsRNA ratio) will be in the range of from about 1:1 to about 50:1, from about 1:1 to about 25:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1. Ranges intermediate to the above recited ranges are also contemplated to be part of the invention.
The cationic lipid can be, for example, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(I -(2,3dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N-(I -(2,3- dioleyloxy)propyl)Ν,Ν,Ν-trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3- dioleyloxy)propylamine (DODMA), l,2-DiLinoleyloxy-N,N-dimethylaminopropane (DLinDMA), 1,2-Dilinolenyloxy-N,Ndimethylaminopropane (DLenDMA), 1,2-Dilinoleylcarbamoyloxy-3-dimethylaminopropane (DLinC-DAP), l,2-Dilinoleyoxy-3-(dimethylamino)acetoxypropane (Dlin-DAC), l,2-Dilinoleyoxy-3morpholinopropane (DLin-MA), l,2-DiIinoleoyl-3-dimethylaminopropane (DLinDaP), 1,2DiIinoleylthio-3 -dimethylaminopropane (DLin-S-DMA), 1 -linoleoyl-2-linoleyloxy-3 10 dimethylaminopropane (DLin-2-DMAP), l,2-Dilinoleyloxy-3-trimethylaminopropane chloride sait (DLin-TMA.Cl), l,2-DilinoleoyI-3-trimethylaminopropane chloride sait (DLin-TAP.Cl), 1,2Dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPz), or 3-(N,N-Dilinoleylamino)-l,2propanediol (DLinAP), 3-(N,N-Dioleylamino)-l,2-propanedio (DOAP), l,2-Dilinoleyloxo-3-(2-N,Ndimethylamino)ethoxypropane (DLin-EG-DMA), l,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA), 2,2-Dilinoleyl-4-dimethylaminomethyl-[l ,3]-dioxolane (DLin-K-DMA) or analogs thereof, (3aR,5s,6aS)-N,N-dimethyl-2,2-di((9Z,12Z)-octadeca-9,12-dienyl)tetrahydro-3aHcyclopenta[d][l,3]dioxol-5-amine (ALN100), (6Z,9Z,28Z,3 lZ)-heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate (MC3), 1,1 '-(2-(4-(2-((2-(bis(2-hydroxydodecyl)amino)ethyl)(2hydroxydodecyl)amino)ethyl)piperazin-l-yl)ethylazanediyl)didodecan-2-ol (Tech Gl), or a mixture thereof. The cationic lipid can comprise from about 20 mol % to about 50 mol % or about 40 mol % of the total lipid présent in the particle. In other embodiments, the compound 2,2-Dilinoleyl-4dimethylaminoethyl-[l,3]-dioxolane can be used to préparé lipid-siRNA nanoparticles.
In some embodiments, the lipid-siRNA particle includes 40% 2,2-Dilinoleyl-4dimethylaminoethyl-[l,3]-dioxolane: 10% DSPC: 40% Cholestérol: 10% PEG-C-DOMG (mole percent) with a particle size of 63.0 ± 20 nm and a 0.027 siRNA/Lipid Ratio.
The ionizable/non-cationic lipid can be an anionic lipid or a neutral lipid including, but not limited to, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl- phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane-l- carboxylate (DOPEmal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), . distearoyl-phosphatidyl-ethanolamine (DSPE), 16-O-monomethyl PE, 16-O-dimethyl PE, 18-1 -trans PE, 1 -stearoyl-2-oleoyl- phosphatidyethanolamine (SOPE), cholestérol, or a mixture thereof. The non-cationic lipid can be from about 5 mol % to about 90 mol %, about 10 mol %, or about 58 mol % if cholestérol is included, of the total lipid présent in the particle.
The conjugated lipid that inhibits aggregation of particles can be, for example, a polyethyleneglycol (PEG)-lipid including, without limitation, a PEG-diacylglycerol (DAG), a PEGo/
dialkyloxypropyl (DAA), a PEG-phospholipid, a PEG-ceramide (Cer), or a mixture thereof. The PEG-DAA conjugale can be, for example, a PEG-dilauryloxypropyl (Ciz), a PEGdimyristyloxypropyl (Ci4), a PEG-dipalmityloxypropyl (Cie), or a PEG- distearyloxypropyl (C]8). The conjugated lipid that prevents aggregation of particles can be from 0 mol % to about 20 mol % or about 2 mol % of the total lipid présent in the particle.
In some embodiments, the nucleic acid-lipid particle further includes cholestérol at, e.g., about 10 mol % to about 60 mol % or about 48 mol % of the total lipid présent in the particle.
In one embodiment, the lipidoid ND98-4HC1 (MW 1487) (see US20090023673, which is incorporated herein by reference), Cholestérol (Sigma-Aldrich), and PEG-Ceramide Cl6 (Avanti
Polar Lipids) can be used to préparé lipid-dsRNA nanoparticles (i.e., LNP01 particles). Stock solutions of each in éthanol can be prepared as follows: ND98,133 mg/ml; Cholestérol, 25 mg/ml, PEG-Ceramide Cl6,100 mg/ml. The ND98, Cholestérol, and PEG-Ceramide C16 stock solutions can then be combined in a, e.g., 42:48:10 molar ratio. The combined lipid solution can be mixed with aqueous dsRNA (e.g., in sodium acetate pH 5) such that the final éthanol concentration is about
35-45% and the final sodium acetate concentration is about 100-300 mM. Lipid-dsRNA nanoparticles typically form spontaneously upon mixing. Depending on the desired particle size distribution, the résultant nanoparticle mixture can be extruded through a polycarbonate membrane (e.g., 100 nm cut-ofï) using, for example, a thermobarrel extrader, such as Lipex Extrader (Northern Lipids, Inc). In some cases, the extrusion step can be omitted. Ethanol removal and simultaneous buffer exchange can be accomplished by, for example, dialysis or tangential flow filtration. Buffer can be exchanged with, for example, phosphate buffered saline (PBS) at about pH 7, e.g., about pH 6.9, about pH 7.0, about pH 7.1, about pH 7.2, about pH 7.3, or about pH 7.4.
H H
ND98 Isomer I
Formula 1
LNP01 formulations are described, e.g., in WO 2008042973, which is hereby incorporated by reference. .
Additional exemplary lipid-dsRNA formulations are described in Table 1.
Table 1
lonizable/Cationic Lipid cationic lipid/non-cationic lipid/cholesterol/PEG-lipid conjugate Lipid:siRNA ratio
SNALP- 1 1,2-Dilinolenyloxy-N,N- dimethylaminopropane (DLinDMA) DLinDMA/DPPC/ Cholesterol/PEG-cDMA (57.1/7.1/34.4/1.4) lipid:siRNA~7:l
2-XTC 2,2-Dilinoleyl-4-dimethylaminoethyl-[l ,3] dioxolane (XTC) XTC/DPPC/Cholesterol/PEG-cDMA 57.1/7.1/34.4/1.4 lipid:siRNA ~ 7:1
LNP05 2,2-Dilinoleyl-4-dimethylaminoethyl-[ 1,3]dioxolane (XTC) XTC/DSPC/Cholesterol/PEG-DMG 57.5/7.5/31.5/3.5 lipid:siRNA~ 6:1
LNP06 2,2-Dilinoleyl-4-dimethylaminoethyl-[l,3]dioxolane (XTC) XTC/DSPC/Cholesterol/PEG-DMG 57.5/7.5/31.5/3.5 lipid:siRNA~ 11:1
LNP07 2,2-Dilinoleyl-4-dimethylaminoethyl-[ 1,3]dioxolane (XTC) XTC/DSPC/Cholesterol/PEG-DMG 60/7.5/31/1.5, lipid:siRNA~6:l
LNP08 2,2-DilinoIeyl-4-dimethylaminoethyl-[l,3]dioxolane (XTC) XTC/DSPC/Cholesterol/PEG-DMG 60/7.5/31/1.5, lipid:siRNA~ 11:1
LNP09 2,2-Dilinoleyl-4-dimethylaminoethyl-[l,3]dioxolane (XTC) XTC/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA 10:1
LNP10 (3aR,5s,6aS)-N,N-dimethyl-2,2di((9Z,12Z)-octadeca-9,12dienyl)tetrahydro-3aHcyclopenta[d] [ 1,3]dioxol-5-amine (ALN100) ALNIOO/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA 10:1
LNP11 (6Z,9Z,28Z,31 Z)-heptatriaconta-6,9,28,31 tetraen-19-yl 4-(dimethylamino)butanoate (MC3) MC-3/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA 10:1
LNP12 l,l'-(2-(4-(2-((2-(bis(2- hydroxydodecyl)amino)ethyl)(2- Tech Gl/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5
hydroxydodecyl)amino)ethyl)piperazin-1 yl)ethylazanediyl)didodecan-2-ol (Tech _θΏ__ Lipid:siRNA 10:1
LNP13 XTC XTC/DSPC/Chol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA: 33:1
LNP14 MC3 MC3/DSPC/Chol/PEG-DMG 40/15/40/5 Lipid:siRNA: 11:1
LNP15 MC3 MC3/DSPC/Chol/PEG-DSG/GalNAc-PEG- DSG 50/10/35/4.5/0.5 Lipid:siRNA: 11:1
LNP16 MC3 MC3/DSPC/Chol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA: 7:1
LNP17 MC3 MC3/DSPC/Chol/PEG-DSG 50/10/38.5/1.5 Lipid: siRNA: 10:1
LNP18 MC3 MC3/DSPC/Chol/PEG-DMG 50/10/38.5/1.5 Lipid:siRNA: 12:1
LNP19 MC3 MC3/DSPC/Chol/PEG-DMG 50/10/35/5 Lipid:siRNA: 8:1
LNP20 MC3 MC3/DSPC/Chol/PEG-DPG 50/10/38.5/1.5 Lipid:siRNA: 10:1
LNP21 C12-200 C12-200/DSPC/Chol/PEG-DSG 50/10/38.5/1.5 Lipid:siRNA: 7:1
LNP22 XTC XTC/DSPC/Chol/PEG-DSG 50/10/38.5/1.5 Lipid:siRNA: 10:1
DSPC: distearoylphosphatidylcholine
DPPC: dipalmitoylphosphatidylcholine
PEG-DMG: PEG-didimyristoyl glycerol (C14-PEG, or PEG-C14) (PEG with avg mol wt of 2000)
PEG-DSG: PEG-distyryl glycerol (C18-PEG, or PEG-C18) (PEG with avg mol wt of2000)
PEG-cDMA: PEG-carbamoyl-l,2-dimyristyloxypropylamine (PEG with avg mol wt of 2000)
SNALP (I,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA)) comprising formulations are described in International Publication No. WO 2009/127060, filed April 15,2009, which is hereby incorporated by reference.
XTC comprising formulations are described in PCT Publication No. WO 2010/088537, the entire contents of which are hereby incorporated herein by reference.
10 MC3 comprising formulations are described, e.g., in U.S. Publication No. 2010/0324120, the entire contents of which are hereby incorporated by reference.
ALNY-100 comprising formulations are described in PCT Publication No. WO 2010/054406, the entire contents of which are hereby incorporated herein by reference.
C12-200 comprising formulations are described in PCT Publication No. WO 2010/129709, 15 the entire contents of which are hereby incorporated herein by reference.
Compositions and formulations for oral administration include powders or granules, microparticulates, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders can be désirable. In some embodiments, oral formulations are those in which dsRNAs featured in the invention are administered in conjunction with one or more pénétration enhancer surfactants and chelators. Suitable surfactants include fatty acids or esters or salts thereof, bile acids or salts thereof. Suitable bile acids/salts include chenodeoxycholic acid (CDCA) and ursodeoxychenodeoxycholic acid (UDCA), cholic acid, dehydrocholic acid, deoxycholic acid, glucholic acid, glycholic acid, glycodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, sodium tauro-24,25-dihydro-fusidate and sodium glycodihydrofusidate. Suitable fatty acids include arachidonic acid, undecanoic acid, oleic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, l-dodecylazacycloheptan-2-one, an acylcamitine, an acylcholine, or a monoglyceride, a diglyceride or a pharmaceutically acceptable sait thereof (e.g., sodium). In some embodiments, combinations of pénétration enhancers are used, for example, fatty acids/salts in combination with bile acids/salts. One exemplary combination is the sodium sait of lauric acid, capric acid and UDCA. Further pénétration enhancers include polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether. DsRNAs featured in the invention can be delivered orally, in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. DsRNA complexing agents include poly-amino acids; polyimines; polyacrylates; polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates; cationized gelatins, albumins, starches, acrylates, polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates; DEAE-derivatized polyimines, pollulans, celluloses and starches. Suitable complexing agents include chitosan, N-trimethylchitosan, poly-L-lysine, polyhistidine, polyomithine, polyspenmnes, protamine, polyvinylpyridine, polythiodiethylaminomethylethylene P(TDAE), polyaminostyrene (e.g., p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate),poly(butylcyanoacrylate), poly(isobutylcyanoacrylate), poly(isohexylcynaoaciylate), DEAE-methacrylate, DEAE-hexylacrylate, 5 DEAE-acrylamide, DEAE-albutnin and DEAE-dextran, polymethylacrylate, polyhexylacrylate, poly(D,L-lactic acid), poIy(DL-lactic-co-glycolic acid (PLGA), alginate, and polyethyleneglycol (PEG). Oral formulations for dsRNAs and their préparation are described in detail in US Patent Nos. 6,887,906 and 6,747,014, and US 20030027780, each of which is incorporated herein by reference.
Pharmaceutical compositions of the présent invention include, but are not limited to, 10 solutions, émulsions, and liposome-containing formulations. These compositions can be generated from a variety of components that include, but are not limited to, preformed liquide, self-emulsifying solids and self-emulsifying semisolids. Particularly preferred are formulations that target the liver when treating hepatic disorders such as hepatic carcinoma.
The pharmaceutical formulations of the présent invention, which can conveniently be 15 presented in unit dosage form, can be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingrédients with the pharmaceutical carrier(s) or excipient(s). In general, the formulations are prepared by uniformly and intimately bringing into association the active ingrédients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.
V. Uses of the Methods of the Invention
The invention sets forth various methods and treatment regimens. It is understood that the methods can be provided as uses of the RNAi agents and vaccines provided herein. That is, the invention provides
a) an RNAi agent that targets at least three HBV transcripts, wherein the RNAi agent comprises a sense strand and an antisense strand;
b) a protein-based vaccine comprising an HBV core antigen (HBcAg) and an HBV surface antigen (HBsAg); and
c) a nucleic acid-based vaccine comprising an expression vector construct encoding an 30 HBcAg or an HBsAg, wherein the construct encodes a protein that shares an epitope with the proteinbased vaccine; thereby treating the subject for use in methods of treating a subject having a hepatitis B infection.
The uses include ail of the variations and exemplary RNAi agents, protein-based vaccines, and nucleic acid-based vaccines provided herein.
VI. Kits for Practicing the Methods of the Invention
The invention sets forth various methods, treatment regimensm and uses of agents for the treatment of a subject having a hepatitis B infection. It is understood that agents for practicing the methods of the invention can be prepared based in the disclosure provided herein. Such a kit would include,
a) an RNAi agent that targets at least three HBV transcripts, wherein the RNAi agent comprises a sense strand and an antisense strand;
b) a protein-based vaccine comprising an HBV core antigen (HBcAg) and an HBV surface antigen (HBsAg);
c) a nucleic acid-based vaccine comprising an expression vector construct encoding an HBcAg or an HBsAg, wherein the construct encodes a protein that shares an epitope with the proteinbased vaccine; thereby treating the subject; and 10 Φ instructions for use in methods of treating a subject having a hepatitis B infection.
The uses include ail of the variations and exemplary RNAi agents, protein-based vaccines, and nucleic acid-based vaccines provided herein. The components of the kit may be provided together, e.g., in a box. In certain embodiments, the components of the invention may be provided separately, e.g., due to different storage requirements, but be provided for use together, e.g., based on 15 package instructions for use.
This invention is further illustrated by the following examples which should not be construed as limiting. The entire contents of ail references, patents and published patent applications cited 20 throughout this application, as well as the Figures, Appendix A, and the Sequence Listing, are hereby incorporated herein by reference.
EXAMPLES
Example 1. Materials and methods
Exemplary iRNAs
Exemplary iRNA target sites and unmodified and modified siRNA sequences are provided in the tables in Appendix A.
The chemically modified HBV-siRNA duplexes used in the experiments below hâve the following sequences:
DupIexID Sense Sequence Unmodified (5’ to 3’) SEQ ID: Antisense Sequence Umodified (5’ to 3’) SEQ ID:
AD-66810 GUGUGCACUUCGCUUCACA 27 UGUGAAGCGAAGUGCACACUU 25
AD-66816 CACCAUGCAACUUUUUCACCU 28 AGGUGAAAAAGUUGCAUGGUGUU 26
• 87 ______Modified sequences:
DupIexID Sense Sequence Modified (5’ to 3’) SEQ ID: Antisense Sequence Modified (5’ to 3’) SEQ ID:
AD-66810 j;susguGfcAfCiUfucgcuucacaL96 37 usGfsugaAfgCfGfaaguGfcAfcacsusu 30
AD-66816 csasccauGfcAfAfCfuuuuucaccuL96 38 asGfsgugAfaAfAfaguuGfcAfiiggugsusu 32
Abbreviations for nucléotide monomers in modified nucleic acid sequences are provided in Table 1 of Appendix A.
The target site of AD-66810 is GTGTGCACTTCGCTTCACA (SEQ ID NO: 39) which is nucléotides 1579-1597 ofNC_003977.1 (SEQIDNO: 1).
The target site of AD-66816 is CACCATGCAACTTTTTCACCT (SEQ ID NO: 40) which is nucléotides 1812-1832 ofNC_003977.1 (SEQIDNO: 1).
Cell Culture Evaluation of HBV-siRNA hNTCP-expressing HepG2 cells were infected (100 multiplicity of infection (MOI)) HBV particles/cell (subtype ayw)) in duplicate. At day 4 after infection, cells were trypsinized and reseeded into multiwell plates and transfected with control or HBV-siRNAs AD-66810 (having the Chemical modifications shown in the table above and sense and antisense sequences as set forth in
SEQ ID NOs: 37 and 30, respectively) or AD-66816 (having the Chemical modifications shown in the table above and sense and antisense sequences as set forth in SEQ ID NOs: 38 and 32, respectively) each delivered at 100 nM, 10 nM, or 1 nM using Lipofectamine® RNAiMax. Supematant was harvested at days 3, 6,10,13, and 17 after reseeding and HBeAg and HBsAg levels were determined relative to non-transfected control. HBsAg and HBeAg levels were determined using a chemiluminescent microparticle immunoassay (CMIA) measured in an Abbott Architect immunoassay analyzer (Abbott Laboratories, Abbott Park, IL, USA).
Mice, siRNA Administration, and Vaccinations
HBV-transgenic mice (StrainHBV1.3xfs (HBV génotype D, subtype ayw)), were derived 25 from in-house breeding under spécifie pathogen-free conditions following institutional guidelines.
For siRNA administration, mice were subcutaneously administered a 3 mg/kg or 9 mg/kg dose of control siRNA or HBV-siRNA (modified AD-66810 or modified AD-66816); or intravenously administered by tail vein injection 1 x 10n AAV particles for expression of the HBVshRNA as indicated in the Figures and Examples below.
For protein vaccinations, mice were immunized subcutaneously with recombinant yeast
HBsAg and Escherichia coli HBeAg (APP Latvijas Biomedicinas, Riga, Latvia) mixed with 31.91 pg of synthetic phosphorothioated CpG ODN 1668 and 25 pg poly[di(sodiumcarboxylatoethylphenoxy)phosphazene] (PCEP) in 50 pl PBS.
Recombinant MVA were generated by homologous recombination and host range sélection as described previously (Staib et al., 2003. Biotechniques. 34:694-700). The entire HBeAg (génotype D, subtype ayw) and HBsAg open reading frames (génotype A, subtype ayw or adw) were cloned into MVA transfer plasmids pIIIAHR-PH5 or pIIIAHR-P7.5, thereby placing the HBV proteins under the control of the early/late Vaccinia virus-specific promoters PH5 (HBeAg ayw /HBsAg ayw/HBsAg adw) or P7.5 (HBsAg ayw). After construction of each virus, gene expression, sequence of inserted DNA, and viral purity were verified. For génération of vaccine préparations, MVA were routinely propagated in CEF, purified by ultracentrifugation through sucrose, reconstituted in 1 mM Tris-HCl pH 9.0 and titrated following standard methodology (Staib et al., 2004. Methods Mol Biol. 269:77100). For MVA vaccination, mice were vaccinated intraperitoneally with 1 χ 108 infections units of respective recombinant MVA in 500 μΐ PBS.
Spécifie dosing regimens are provided in the Examples below and in Figures 3,7, and 12.
Serological analysis
Sérum levels of HBsAg and HBeAg were determined in 1:33 dilutions; and anti-HBs levels were determined in a 1:100 dilution using chemiluminescent microparticle immunoassay (CMIA) measured in an Abbott Architect immunoassay analyzer (Abbott Laboratories, Abbott Park, IL, USA). Quantification of sérum HBV titers by real-time polymerase chain reaction and détermination of HBV DNA levels in sérum was performed as described in Untergasser et al., 2006 (Hepatology. 43:53947). The amount of HBV DNA was normalized to DNA level prior to treatment.
Levels of anti-HBc antibodies were determined in 1:20 dilution using the Enzgnost anti-HBc monoclonal test on the ΒΕΡΠΙ platform (Both Siemens Healthcare, Eschbom, Germany). If a sample was measured outside the linear range, higher or lower dilutions were used as appropiate.
Quantification of sérum HBV titers by real-time polymerase chain reaction and détermination of HBV DNA levels in sérum was performed as described in Untergasser et al., 2006 (Hepatology. 43:539-47). The amount ofHBV DNA was normalizedto DNA levelprior to treatment.
ALT activity was measured at the day of bleeding in a 1:4 dilution in phosphate buffered saline (PBS) using the Reflotron GPT/ALT test (Roche Diagnostics, Mannheim, Germany).
Lymphocyte stimulation assay
Liver-associated lymphocytes (LAL) were isolated as described in Stross et al., 2012 (Hepatology 56:873-83) and stimulated with H2-kb-or H-2Db-restricted peptides (see Backes, 2016) for 12 hours in the presence of 1 mg/ml Brefeldin A (Sigma-Aldrich, Taufkirchen,Germany). Cells were live/dead-stained with ethidium monoazidebromide (Invitrogen®, Karlsruhe, Germany) and blocked with anti-CD 16/CD32-Fc-Block (BD Biosciences, Heidelberg, Germany). Surface markers were stained with PB-conjugated anti-CD8-alpha and PE-conjugated anti-CD4 (eBiosciences, Eching, Germany). Intracellular cytokine staining (ICS) was performed with FITC anti-IFN-gamma (XMG1.2), PE-Cy7 anti-TNF-alpha and APC anti-IL-2 (eBiosciences, Ech-ing, Germany) using the
Cytofix/Cytoperm kit (BD Biosciences, Heidelberg, Germany) according to the manufacturées recommendations. The same data were analyzed twice, the second time with a more rigorous exclusion of dead cells.
Immunohistochemical stainings for HBc-expressing hépatocytes
Livers were harvested, fixed in 4% paraformaldéhyde, and paraffin-embedded. The liver was sectioned (2 pm) and sections were stained with rabbit anti-HBcAg as the primary antibody (Diagnostic Biosystems, Pleasanton, CA; #RP 017; 1:50 dilution; retrieval at 100°C for 30 min with EDTA) and a horseradish peroxide coupled secondary antibody. Incubation in Ventana buffer 10 and staining were performed on a NEXES immunohistochemistry robot (Ventana Instruments) using an IVIEW DAB Détection Kit (Ventana Instruments) or on a Bond MAX (Leica Biosystems). For analysis, slides were scanned using a SCN 400 slide scanner and positive cells were counted using the integrated Tissue AI software (both Leica Biosystems).
HB V transcripts from liver lysate
For analysis of HBV RNA from liver lysate, RNA was extracted from 30 mg liver tissue with the RNeasy mini kit (Qiagen) and cDNA was synthesized with the Superscript ΙΠ kit (Thermo Fisher Scientific). HBV transcripts were amplified with primers spécifie for only the 3.5 kb transcripts (forward primer 5’- GAGTGTGGATTCGCACTCC-3’ (SEQ ID NO: 41); reverese primer 5’20 GAGGCGAGGGAGTTCTTCT-3’ (SEQ ID NO: 42)), or with primers binding to the common 3' end of ail HBV transcripts (forward primer 5’- TCACCAGCACCATGCAAC-3’ (SEQ ID NO: 43); reverse primer 5’- AAGCCACCCAAGGCACAG-3’ (SEQ ID NO: 44)) (Dénaturation: 95°C 5 min; Amplification: 95°C 3s, 60°C 30s (40 cycles)) (Yan et al., 2012). Results were normalised to murine GAPDH expression (forward primer 5’- ACCAACTGCTTAGCCC-3’ (SEQ ID NO: 45); reverse primer 5’- CCACGACGGACACATT-3’ (SEQ ID NO: 46)) (Dénaturation: 95°C 5 min; Amplification: 95°C 15s, 60C° 10s, 72°C 25s (45 cycles)). Ail PCR reactions were performed on a LightCycler 480 (Roche Diagnostics).
AA V-HB V mouse model
For the AAV mouse model, wildtype C57/B16 mice (9 weeks of âge; 6 animais per treatment group) were injected i.v. with 2xlO10 genome équivalents (geq) of Adeno-Associated-Virus Serotype 8 (AAV8) carrying a 1.2-fold overlength HBV genome of génotype D (AAV-HBV1.2) (day -28) (see, e-S·, Yang, et al. (2014) Cell and Mol Immunol 11:71) . Starting 4 weeks after AAV-transduction (day 0), animais were treated with 3 injections (3 mg/kg bw, n=12 per group) of either a control siRNA, or HBV siRNA (AD-66816 or AD-66810) (days 0, 29, and 57). Each siRNA treatment group ' was divided into two groups (n = 6 per group) to be not treated or treated with the vaccine regimen consisting of recombinant HBsAg, HBcAg (15 pg of each) and 10 pg c-di-AMP given at day 57 and and boostedwithMVA-HBs andMVA-HBc (5xl07 geq ofeach) at day 84. A schematic showing the treatment regimen is provided in Figure 12.
Example 2 - Evaluation of HBV-siRNA in HepG2-NTCP Cell Culture and Dose Finding 5 Experiments in HBVxfs Mice
Anti-HBV siRNAs were evaluated for efficient knockdown of HBV antigens and DNA in an in vitro infection model using HBV-infected HepG2-NTCP cells treated with 1 ’nM, 10 nM, or 100 nM of one of modified AD-66810 or modified AD-66816 HBV-siRNA, or a control siRNA as provided above. Supematants were collected at days 3,6,10,13, and 17 days after siRNA treatment 10 and assayed for HBeAg and HBsAg levels as compared to untransfected control. Both HBV-siRNAs were demonstrated to effectively knockdown expression of both HBeAg and HBsAg with the highest levels of knockdown observed at days 13 and 17. No significant knockdown was observed with the control siRNA. These data demonstrate that the AD-66810 or AD-66816 HBV-siRNAs are effective at knocking down expression of HBV antigens in a sustained manner in an in vitro System of HBV 15 infection.
The HBV and control siRNAs were then tested in the HBVxfs transgenic model of chronic hepatitis B. The HBVxfs mice include an integrated HBV genome that is expressed under the control of a liver-specific promoter. At about 10 weeks of âge, mice were administered a 3 or 9 mg/kg dose of one of AD-66810 or AD-66816 HBV-siRNA or a control siRNA (n = 6 per group). Blood samples 20 were collected at days 6,13, and 21 after siRNA treatment and sérum was prepared. HBeAg, HBsAg, and HBV DNA levels in sérum (Figures 2A-2C) were determined as provided above. Further, RNA was isolated from liver and total HBV RNA and HBV 3.5 kB transcript levels were detected using the method of Yan, 2012 and normalized to GAPDH expression (Figures 2D and 2E).
Both of the HBV-siRNAs at both doses were demonstrated to effectively knockdown 25 expression of HBsAg and HBeAg and to decrease HBV DNA levels in sérum as compared to control levels (see Figures 2A-2C). Futher, total liver HBV RNA relative to GAPDH DNA and 3.5 kb HBV RNA relative to GAPDH RNA levels were strongly decreased by both doses of the HBV siRNAs as compared to control levels (Figures 2D and 2E). Based on these results, the 3 mg/kg dose was selected for use in further experiments.
Example 3 - Comparison of Reducing Antigen Load with siRNA to Nucleot(s)ide Analogs Prior to Therapeutic Vaccine Administration in an HBV Transgenic Mouse Model
Having demonstrated that siRNA targeted to HBV can effectively knockdown expression of HBsAg and HBeAg and decrease HBV DNA levels in sérum in the HBVxfs mouse model, the effect 35 of treatment of mice with the nucleoside analog Entecavir or HBV-siRNA prior to therapeutic vaccine administration using a prime-boost regimen was tested. The treatment scheme is shown in Figure 3.
Mice were pretreated with one of six treatment regimens prior to vaccination using a primeboost regimen (n= 6 per group):
(1) No pretreatment;
(2) Entecavir at 1 pg/ml in water throughout the course of the study beginning on the first day of Week 0 (expected dose of about 4 mg/day based on calculations provided in Lütgehetmann et al., 2011, Gastroenterology. 140:2074-83);
(3) A 3 mg/kg dose on the first day of Weeks 0,4, 8, and 12 of the control iRNA agent.
(4) A single dose on the first day of Week 0 with an expression vector encoding an shRNA targeted to HBV (HBV-shRNA) (Michler et al., 2016); or (5-6) A 3 mg/kg dose on the first day of Weeks 0,4,8, and 12 of modified AD-66816 or modified AD-86610 (generically HBV-siRNA).
On the first day of Weeks 12 and 14, a mixture of recombinantly expressed yeast HBsAg (15 pg) andE. coli expressed HBeAg (15 pg) adjuvanted with 31.9 pg synthetic phosphorothioated CpGODN 1668 (CpG) and 25 pgpoly[di(sodiumcarboxylatoethyl-phenoxy)phosphazene] (PCEP) was subcutaneously administered to ail mice as a protein-prime vaccination (Backes, 2016).
On the first day of week 16, a mixture of modified vaccinia viruses Ankara expressing 15 HBsAg or HBeAg (5 x 107 particles of each virus) was subcutaneously administered to ail mice as a boost vaccination (Backes, 2016).
Blood samples were obtained on the first days of Week 0,2,4, 8,12,16, and 17 and sérum samples prepared therefrom were assayed for levels of HBsAg, HBeAg, and HBV DNA. Results are shown in Figure 4.
HBsAg and HBeAg levels mice in groups 1,2, and 3 (mock, Entecavir, control iRNA agent) were similar. The HBV-shRNA or HBV-siRNAs (AD-66816 or AD-86610) alone caused a significant decrease in HBsAg, HBeAg, and HBV DNA in sérum (Figures 4A-4C). The three dose prime-boost vaccination scheme resulted in a further decrease in HBsAg in ali groups, and reduced the level of HBsAg in at least some animais in the HBV-shRNA and HBV-siRNA groups to below the level of détection. However, vaccine treatment did not decrease HBeAg levels in any of the groups. Without being bound by mechanism, it is proposed that the decrease in HBsAg, but not HBeAg, results from the immune response induced by the vaccine against the s antigen, but not the e antigen, which is produced by proteolytic processing of the C protein (see Figure 5 discussed below).
HBV DNA levels were decreased to about the lower limit of quantitation with Entecavir alone 30 so no effect of the three dose prime-boost vaccine could be detected (Figure 4C). Mock treatment and treatment with the HBV-shRNA, the HBV-siRNAs, and control siRNA ail decreased HBV DNA levels and the level of HBV-DNA was further decreased by the prime-boost vaccine in ail groups. It is unclear why the mock treatment and control siRNA decreased HBV DNA levels in this experiment. No decrease in HBV DNA was observed in response to treatment with control siRNA in other experiments (see, e.g., Figures 2C and 8C). These data demonstrate that RNAi is superior to nucleot(s)ide analog therapy in reducing viral antigens. Also, RNAi and subséquent vaccination hâve a combined effect on HBsAg and HBV DNA levels greater than either agent alone.
On the final day of the experiment (first day of Week 17), mice were sacrificed and their livers harvested. Liver associated lymphocytes were isolated from liver and afier peptide stimulation CD8+ T cell responses measured via intracellular cytokine staining. Specifically, intrahepatic CD8+ T cell responses were assessed for response to HBsAg, HBcAg, and the MVA virus particle using the method provided in Backes, 2016. The data were analyzed twice using two different thresholds for the exclusion of dead immune cells as the exclusion of dead immune cells in the first analysis provided in Figures 5A-5C was determined to be insufïicient. The second analysis is presented in Figures 5D-5F. The second analysis confirmed the conclusions from the first analysis.
Mice pretreated with the HBV-shRNA or the HBV-siRNAs before vaccination were able to generate a CD8+ T cell immune response against the HBsAg and HBcAg (Figures 5A, 5B, 5D, and 5E) indicating that cytotoxic T cells able to clear HBV infection are induced when HBV antigen levels are suppressed prior to vaccination. No signifîcant CD8+ T cell immune response against the HBV antigens was observed in the mock, Entecavir, or control siRNA groups. A signifîcant and similar CD8+ T cell immune response against the MVA virus in ail animais, independent of pretreatment or viral antigen levels, demonstrated that vaccination had worked equally well in ail animais and was not influenced by HBV antigen levels, thereby demonstrating the presence of a competent immune system (Figures 5C and 5F). No signifîcant différences in antibody production were observed between mock treated animais and any of the other groups indicating that high HBV antigen levels may induce T cell tolérance.
These data demonstrate that RNAi treatment, in contrast to the current standard of care treatment with a nucleoside analog, can restore HBV-specific T cell immunity in the liver and enable the induction of HBV-specific CD8+ T cell responses after therapeutic vaccination. A robust CD8+ effector T cell response has been associated with viral clearance and ftinctional cure (see, e.g., Thimme et al., 2003. J. Virol. 77:68-76, and Backes et al., 2016. Vaccine. 34:923-932).
RNA was also isolated from liver and total HBV RNA and HBV 3.5 kB transcript levels were detected using the method of Yan, 2012 and normalized to GAPDH expression. Treatment of mice with HBV-siRNA or HBV-shRNA prior to vaccine administration resulted in a signifîcant decrease in HBV total RNA and HBV 3.5 kb transcript as compared to the mock treated control (Figures 6A and 6B). No signifîcant change in HBV total RNA and HBV 3.5 kb transcript was observed in the mice treated with Entecavir or the control siRNA prior to vaccination as compared to the mock treated control. These data demonstrate that both HBV siRNAs and the shRNA, in contrast to the control and Entecavir groups, successfully led to a decrease in HBV transcript levels.
Further, expression of HBV antigens in the liver was analyzed by immunohistochemical staining for HBc of liver sections and counting of HBc positive cells per mm2 (Figure 6C). Only groups of animais pre-treated with HBV siRNA or shRNA, but not Entecavir or the control siRNA, showed reduced HBc expression following vaccination.
Throughout the experiment, body weight and ALT levels were monitored. No signifîcant différences were observed in any of the treatment groups as compared to mock treated control.
Example 4 — Evaluation of the Effect of Duration of HBV Antigen Knockdown on Response to Immunization in an HBV Transgenic Mouse Model
Having demonstrated that suppression of expression of HBV antigens using shRNA or siRNA 5 is effective at potentiating an immune response to an HBV vaccine regimen, a study was designed to détermine if the length of time of HBV antigen suppression had an effect on potentiation of an HBV immune response. A treatment scheme is shown in Figure 7.
Using the HBV1.3xfs mouse model, mice were treated for eight, six, or three weeks with HBV-siRNA AD-66816 (modified) or the control siRNA for 8 weeks, administered subcutaneously at 10 3 mg/kg/dose. siRNA administration was followed by administration of the prime-boost vaccine regimen as set forth above with the exception that c-di-AMP was used as an adjuvant with protein administration rather than PCEP + CPG (n= 6 per group). Therefore, mice in the 8 week group (n = 6) received three doses of siRNA with the third dose being administered on the first day of vaccine administration. The mice in the 6 week group (n = 12) received two doses of siRNA with the second 15 dose being administered two weeks prior to the first day of vaccine administration. Finally, the mice in the 3 week group (n = 6) received one dose of siRNA with the dose being administered three weeks prior to the first day of vaccine administration.
Blood samples were collected on the first day of -8 weeks, -6 weeks, -4 weeks, -2 weeks, 0 weeks, 2 weeks, 4 weeks, and 6 weeks, before (négative numbers) and after the first dose of vaccine 20 administration on the first day of Week 0. Sérum was prepared and HBsAg, HBeAg, and HBV DNA levels were assessed as provided above.
A significant decrease in each HBsAg, HBeAg, and HBV DNA was observed after the first administration of AD-66816 (Figures 8A-8C). A further significant decrease in HBsAg was observed after treatment with the vaccine boost, with the greatest decrease observed in the 8 week pretreatment 25 group to below the level of détection of the assay, representing a greater than 5 loglO decrease in HBsAg level in ail treated animais. Immunization caused only slight further réductions (<0.5 loglO) of HBV DNA which had been significantly decreased by the siRNA treatment. No further decrease in HBeAg levels was observed in response to the vaccination regimen.
These data demonstrate that efïïcacy of therapeutic vaccination correlates with duration of 30 antigen suppression before start of vaccination. Reconstitution of HBV-specifïc CD8+ T cell responses takes several weeks, with a 6 or preferably 8 week pretreatment rather than a 3 week pretreatment.
On the final day of the experiment, on the first day of Week 6 after the start of immunization, mice were sacrifïced and their livers harvested for six mice from each group. Liver associated lymphocytes were isolated and a lymphocyte stimulation assay was performed as provided above. Specifically, intrahepatic CD8+ T cell responses were assessed for response to HBsAg, HBcAg, and the MVA virus particle using the method provided in Backes, 2016. T-cell responses against HBsAg and HBcAg in liver corresponded with the duration of HBV antigen knockdown, with a trend of
higher levels of immune response observed with longer duration of HBV antigen resulting in greater T-cell response (see Figures 9A-9C). Similar responses to MVA virus antigens were observed across ail groups, independent of pretreatment, showing that vaccination had worked equally well in ail animais and was not influenced by HBV antigen levels demonstrating the presence of a competent 5 immune System (Figure 9D). No significant différences in antibody production were observed between control siRNA treated animais and any of the other groups. This demonstrates, that reconstitution of HBV-specific CD8+ T cell responses does not occur immediately, with stronger responses seen after therapeutic vaccination if animais had lowered HBV antigen titers for at least 6 or 8 weeks compared to only 3 weeks. It further confirais the previous finding that, in contrast to T cell 10 responses, B cell immunity does not seem to be significant influenced by HBV antigen titers.
RNA was also isolated from liver and total HBV RNA and HBV 3.5 kB transcript levels were detected using the method of Yan, 2012 and normalized to GAPDH expression. Treatment of mice with HBV-siRNA AD-66816 prior to vaccine administration resulted in a significant decrease in HBV total RNA and HBV 3.5 kb transcript in liver lysâtes as compared to the control siRNA treated control 15 (Figures 10A and 10B). Further, HBV antigen expression in the liver was analyzed by immunohistochemical staning and counting of HBc positive cells per mm2 (Figure 10C). Correlating the observed increase in HBV-specific CD8 responses with increased duration of siRNA pretreatment, decreased numbers of HBc expressing cells where observed in the liver. These results demonstrate that the CD8+ T cell responses did prevent antigen expression in the liver..
To assess the durability of response, blood samples were collected from mice pretreated with the AD-66816 HBV-siRNA using the six week treatment regimen at 2 and 3 weeks after administration of the boost vaccination (Figures 11A-1 ID). In three of the six mice, HBsAg levels continued to drop to below the level of détection of the assay (Figure 11 A). No similar decrease in HBeAg levels were observed during the course of the experiment (Figure 1 IB). These data show that 25 the maximum effect by the siRNA-vaccination combinatorial therapy provided herein is later than 1 week after the MVA vaccination, which was chosen as termination time point to best asses CD8+ T cell responses. Anti-HBs antibody response (Figure 1 IC) and T cell immune response in the liver against HBs(S208) (Figure 1 ID) at week 7 after the first vaccine dose after the 6 week regimen in the dosing regimen. The antibody response varied among animais.
These data demonstrate that a functional cure is possible using the treatment regimens provided herein. Further, these data suggest that a lower HBsAg and HBeAg burden can resuit in a greater level of immune clearance of HB antigens and potentiate an immune response, at least within the short time course of the experiment.
Throughout the experiment, body weight and ALT levels were monitored. No significant 35 différences were observed in any of the treatment groups as compared to mock treated control.
Example 5 - Evaluation of the Effect of Duration of HBV Antigen Knockdown on Response to Immunization in an AAV-HBV Mouse Model
Having demonstrated the efficacy of the siRNA-vaccine combination treatment regimen in a transgenic mouse model, an AAV-HBV infection mouse model was used to study the efficacy of the 5 treatment regimen in acquired infection model (see, e.g., Yang, et aï. (2014) Cell Mol Immunol 11:71). This mouse model exhibits sustained HBV viremia after infection with a recombinant adenoassociated virus (AAV) carrying a replicable HBV genome.
There are a number of différences between the HBV-transgenic and AAV-HBV mouse models. The HBV transgenic mice can express HBV antigens essentially from birth, whereas the 10 AAV-HBV model allows for the introduction of the HBV genome at a later time in the life of the mice. This may hâve an effect on immune tolérance. Further, the HBV transgenic mice carry the transgene in every cell of the body, providing the possibility of “leaky” extrahepatic expression. Although the AAV8 serotype could infect cells outside of the liver, it has a strong liver tropism. Moreover, it is not possible to clear an HBV infection in a transgenic mouse. When a transgenic 15 HBV expressing liver cell is killed, it is replaced by a new HBV expressing cell. In the infection model, if the infected cells are killed, the newly dividing cells are not infected at the time of cell division.
Nine week old C57/B16 mice were infected with AAV-HBV (- 28 days). Mice were then treated with one of control siRNA, or one of two HBV-siRNAs, modified AD-66816 or modified AD20 66810 at 3 mg/kg administered subcutaneously on days 0,29, and 57 (i.e., 0 weeks, 4 weeks, 8 weeks) (n= 12 per group). Each siRNA treatment group was divided into two groups (n=6 per group). One group was treated with the HBV vaccine protocol (protein prime on days 57 and 70, and MVA boost on day 84, i.e., weeks 8, 10, and 12, respectively) and one group was not. A schematic showing the dosing regimen is provided in Figure 12. Mice were monitored throughout the experiment for sérum 25 HBsAg, HBeAg, anti-HBs antibodies, body weight, and ALT. Anti-HBe antibody levels were also periodically tested.
Figures 13A and 13B show an increase in HBsAg and HBeAg levels comparable to that seen in transgenic mice within two weeks of transduction with the AAV-HBV virus. Mice treated only with the control siRNA replicated HBV for greater than 8 months at levels comparable to chronically 30 infected humans (HBsAg levels around 2,000 lU/ml, HBV viremia 10^107 lU/ml). HBV siRNAs AD-66816 and AD-66810 reduced HBsAg by 2 and 2.5 logio, respectively, and HBeAg by >1 logio. The effect persisted for at least 4 weeks after stopping siRNA treatment before antigenemia slowly rebounded to baseline levels after 18 weeks (Figures 13A andl3B).
Intrahepatic HBV DNA (Figure 13D) and AAV DNA (Figure 13E) levels were determined at 35 week 22 by qPCR as described above. The relative expression in liver of HBV 3.5 RNA relative to GAPDH RNA (Figure 13F) and total HBV RNA relative to GAPDH RNA (Figure 13G) were determined using rtPCR. Mice treated with the combined siRNA-vaccine protocol demonstrated a signifîcant decrease in total HBV DNA and AAV DNA as compared to untreated control or siRNA or vaccine treatement alone at the 22 week time point (Figures 13D and 13E). Notably, total HBV DNA levels dropped to less than one copy per cell as a resuit of the combination treatment (Figure 13D). Mice treated with the combined siRNA-vaccine protocol also demonstrated a significant decrease level of HBV 3.5 kb RNA expression relative to GAPDH RNA expression as compared to ail other treatment regimens (Figure 13F). A significant decrease in total HBV RNA relative to GAPDH RNA expression was observed as compared to treatment with vaccine or siRNA alone (Figure 13G). These data suggest that a short course of administration of siRNA alone or a therapeutic vaccine against HBV is insufficient to durably suppress HBV infection. Immune mediated control of HBV after siRNA knockdown of HBV expression is long lasting. At 22 weeks after the last siRNA dose, the effect of the siRNA was waning as seen in the groups which had only received the HBV siRNAs without vaccination. Mice treated with the siRNA-vaccine protocol maintained HBV DNA and RNA suppression long after the end of siRNA administration.
No immune responses were observed in these fully immune competent mice under siRNA treatment alone, but vaccine treatment resulted in anti-HBs séroconversion in ail vaccinated animais (Figures 14A and 14B). siRNA-pretreated animais, however, developed 10-fold higher and more constant anti-HBs titers and were able to completely and persistently clear sérum HBsAg and HBeAg. In contrast, anti-HBe séroconversion was only observed in antimals pretreated with HBV siRNAs. Interestingly, three of the 12 mice vaccinated after HBV siRNA treatment showed a transient relapse of HBeAg between week 15 and 22 co-inciding with decreased levels of anti-HBe (Figure 13C). Without being bound by mechanism, it is proposed that theHBeAg relapse was controlled by a memory immune response induced by the vaccine. Taken together, suppression of HBV antigen expression by an siRNA in combination with a heterologous prime-boost vaccine is sufficient to break immune tolérance to HBV antigens. The sequential therapy achieved long-term functional cure in a mouse model of persistent HBV infection without causing significant liver damage.
Figures 14A and 14B show that animais treated with HBV siRNA plus the vaccine regimen developed high titers of anti-HBs antibodies and anti-HBe antibodies. The level of anti-HBs antibodies continued to increase after the last vaccine dose. Although anti-HBs antibodies could also be measured in animais that received the control siRNA plus the vaccine regimen, the levels were signifîcantly lower. Further, only animais that received HBV siRNA plus the vaccine regimen developed anti-HBe antibodies and achieved anti-HBe séroconversion. The combinatorial therapy using siRNA and vaccine appeared to be well tolerated. Ail mice equally gained weight and only a mild ALT élévation (<2-fold upper limit of normal) was observed (Figures 15A and 15B). The loss of antigenemia concided with slight increases of ALT activity seen in treatment groups which had received HBV siRNA in conjunction with the vaccination regimen (Figure 15 A). These groups showed significant but mild increases (both p>0.05 or smaller by repeated measure two-way ANOVA; only comparing time points after start of vaccination) as compared to ail other treatment groups that did not receive the combination HBVsiRNA-vaccine regimen. There was a steady increase in body weight in ail animais throughout the experiment independent of siRNA treatment.
Animais that were vaccinated showed a slight and transient decrease (approximately 5%) of body weight after vaccination, but rebounded to normal levels within nine days and subsequently gained weight comparable to the control groups (Figure 15B).
Without being bound by mechanism, the data provided herein strongly suggest that the high level of HBV antigen expression routinely detected as circulating HBsAg and HBeAg prevents HBVspecific CD8+ T cell responses, which has far reaching conséquences for future immune therapy of chronic hepatitis B. Using 2 different mouse models for chronic hepatitis B, it is proposed that HBVspecific immunomodulation can be reverted by suppressing HBV protein expression in hépatocytes using an RNAi-based therapy. Such réduction of HBV antigens by RNAi, in contrast to standard-of10 care nucleo(t)side analogues, allows for induction of strong HBV-specific CD8+ T cell responses by therapeutic vaccination that are required for control of HBV infection.
APPENDIXA
Table 1. Abbreviations of nucléotide monomers used in nucleic acid sequence représentation. It will be understood that, unless otherwise indicated, these monomers, when présent in an oligonucleotide, are mutually linked by 5'-3'-phosphodiester bonds.___________________________________________
Abbreviation Nucleotide(s)
A Adenosine-3 ’-phosphate
Af 2’-fluoroadenosine-3 ’-phosphate
Afs 2’-fluoroadenosine-3’-phosphorothioate
As adenosine-3’-phosphorothioate
C cytidine-3 ’-phosphate
Cf 2 ’-fluorocytidine-3 ’-phosphate
Cfs 2’-fluorocytidine-3’-phosphorothioate
Cs cytidine-3 ’-phosphorothioate
G guanosine-3 ’-phosphate
Gf 2’-fluoroguanosine-3’-phosphate
Gfs 2’-fluoroguanosine-3 ’-phosphorothioate
Gs guanosine-3 ’-phosphorothioate
T 5 ’-methyluridine-3 ’-phosphate
Tf 2’-fluoro-5-methyluridine-3’-phosphate
Tfs 2’-fluoro-5-methyluridine-3’-phosphorothioate
Ts 5-methyluridine-3 ’-phosphorothioate
U Uridine-3 ’-phosphate
Uf 2 ’-fluorouridine-3 ’-phosphate
Ufs 2’-fluorouridine -3’-phosphorothioate
Us uridine -3’-phosphorothioate
N any nucléotide (G, A, C, T or U)
a 2'-O-methyladenosine-3’-phosphate
as 2'-O-methyladenosine-3 ’- phosphorothioate
c 2'-O-methylcytidine-3 ’-phosphate
CS 2'-O-methylcytidine-3 ’- phosphorothioate
g 2'-O-methylguanosine-3 ’-phosphate
gs 2'-O-methylguanosine-3 ’ - phosphorothioate
t 2’-O-methyl-5-methyIuridine-3’-phosphate
ts 2’-O-methyl-5-methyluridine-3’-phosphorothioate
u 2'-O-methyluridine-3 ’-phosphate
us 2'-O-methyluridine-3’-phosphorothioate
s phosphorothioate linkage
Abbreviation Nucleotide(s)
L96 N-[tris(GalNAc-alkyl)-amidodecanoyl)]-4-hydroxyprolinol Hyp-(GalNAc-alkyl)3
(dT) 2 ' -deoxythymidine-3 ' -phosphate
Y34 2-hydroxymethyl-tetrahydrofurane-4-methoxy-3-phosphate (abasic 2'-OMe furanose)
Y44 2-hydroxymethyl-tetrahydrofurane-5-phosphate
(Agn) Adenosine-glycol nucleic acid (GNA)
(Tgn) Thymidine-glycol nucleic acid (GNA) S-Isomer
(Cgn) Cytidine-glycol nucleic acid (GNA)
P Phosphate
VP Vinyl-phosphate
100 w
Table 2. Exemplary Unmodifîed Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ IDNO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-61522 A-123463 AGUUAUAUGGAUGAUGUGGUA 47 A-123464 UACCACAUCAUCCAUAUAACUGA 263 731_753
AD-61547 A-123487 GGAUGUGUCUGCGGCGUUUUA 48 A-l 23488 UAAAACGCCGCAGACACAUCCAG 264 373_395 ' .
AD-63938 A-127896 ACUCGUGGUGGACUUCUCUCA 49 A-127897 UGAGAGAAGUCCACCACGAGUCU 265 250 272
AD-63939 A-127909 ACUCGUGGUGGACUUCUCUCA 50 A-127906 UGAGAGAAGUCCACCACGAGUCU 266 250_272
AD-63940 A-127917 ACUCGUGGUGGACUUCTCUCA 51 A-127906 UGAGAGAAGUCCACCACGAGUCU 267 250_272
AD-63941 A-127905 ACUCGUGGUGGACUUCUCUCA 52 A-127925 UGAGAGAAGUCCACCACGAGUCU 268 250_272
AD-63942 A-127933 UCGUGGUGGACUUCUCUCA 53 A-l 27934 UGAGAGAAGUCCACCACGAGU 269 252_274
AD-63943 A-127944 ACUCGUGGUGGACUUCUCUCA 54 A-127942 UGAGAGAAGUCCACCACGAGUCU 270 250_272
AD-63945 A-127910 ACUCGUGGUGGACUUCUCUCA 55 A-127906 UGAGAGAAGUCCACCACGAGUCU 271 250_272
AD-63946 A-127918 ACUCGUGGUGGACUUCUCUCA 56 A-127906 UGAGAGAAGUCCACCACGAGUCU 272 250_272
AD-63947 A-127905 ACUCGUGGUGGACUUCUCUCA 57 A-127926 UGAGAGAAGUCCACCACGAGUCU 273 250 272
AD-63948 A-127935 GUGGUGGACUUCUCUCA 58 A-l 27936 UGAGAGAAGUCCACCACGA 274 254_276
AD-63949 A-127944 ACUCGUGGUGGACUUCUCUCA 59 A-127906 UGAGAGAAGUCCACCACGAGUCU 275 250_272
AD-63950 A-l 27900 UCGUGGUGGACUUCUCUCAUU 60 A-127901 UGAGAGAAGUCCACCACGAUU 276 252_274
AD-6395Ï A-127911 ACUCGUGGUGGACUUCUCUCA 61 A-127906 UGAGAGAAGUCCACCACGAGUCU 277 250_272
AD-63952 A-127905 ACUCGUGGUGGACUUCUCUCA 62 A-127919 UGAGAGAAGUCCACCACGAGUCU 278 250_272
AD-63953 A-127905 ACUCGUGGUGGACUUCUCUCA 63 A-127927 UGAGAGAAGUCCACCACGAGUCU 279 250_272
AD-63955 A-127945 ACUCGUGGUGGACUUCUCUCA 64 A-127940 UGAGAGAAGUCCACCACGAGUCU 280 250 272
AD-63956 A-127902 UCGUGGUGGACUUCUCUCA 65 A-127903 UGAGAGAAGUCCACCACGAUU 281 252_274
AD-63957 A-127912 ACUCGUGGUGGACUUCUCUCA 66 A-127906 UGAGAGAAGUCCACCACGAGUCU 282 250_272
AD-63958 A-127905 ACUCGUGGUGGACUUCUCUCA 67 A-127920 UGAGAGAAGUCCACCACGAGUCU 283 250_272
AD-63959 A-127905 ACUCGUGGUGGACUUCUCUCA 68 A-127928 UGAGAGAAGUCCACCACGAGUCU 284 250_272
AD-63960 A-126619 UAUUUCCUAGGGUACAA 69 A-127938 UGAGAGAAGUCCACCACGA 285 254_276
AD-63961 A-127945 ACUCGUGGUGGACUUCUCUCA 70 A-127942 UGAGAGAAGUCCACCACGAGUCU 286 250_272
101
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-63962 A-127902 UCGUGGUGGACUUCUCUCA 71 A-127904 UGAGAGAAGUCCACCACGAUU 287 252 274
AD-63963 A-127913 ACUCGUGGUGGACUUCUCUCA 72 A-127906 UGAGAGAAGUCCACCACGAGUCU 288 250 272
AD-63964 A-127905 ACUCGUGGUGGACUUCUCUCA 73 A-127921 UGAGAGAAGUCCACCACGAGUCU 289 250 272
AD-63965 A-127905 ACUCGUGGUGGACUUCUCUCA 74 A-127929 UGAGAGAAGUCCACCACGAGUCU 290 250 272
AD-63966 A-127939 ACUCGUGGUGGACUUCUCUCA 75 A-127940 UGAGAGAAGUCCACCACGAGUCU 291 250 272
AD-63967 A-127945 ACUCGUGGUGGACUUCUCUCA 76 A-127906 UGAGAGAAGUCCACCACGAGUCU 292 250 272
AD-63968 A-127905 ACUCGUGGUGGACUUCUCUCA 77 A-127906 UGAGAGAAGUCCACCACGAGUCU 293 250 272
AD-63968 A-127905 ACUCGUGGUGGACUUCUCUCA 78 A-127906 UGAGAGAAGUCCACCACGAGUCU 294 250 272
AD-63968 A-127905 ACUCGUGGUGGACUUCUCUCA 79 A-127906 UGAGAGAAGUCCACCACGAGUCU 295 250 272
AD-63969 A-127914 ACUCGUGGUGGACUUCUCUCA 80 A-127906 UGAGAGAAGUCCACCACGAGUCU 296 250 272
AD-63970 A-127905 ACUCGUGGUGGACUUCUCUCA 81 A-127922 UGAGAGAAGUCCACCACGAGUCU 297 250 272
AD-63971 A-127905 ACUCGUGGUGGACUUCUCUCA 82 A-127930 UGAGAGAAGUCCACCACGAGUCU 298 250 272
AD-63972 A-127941 ACUCGUGGUGGACUUCUCUCA 83 A-127942 UGAGAGAAGUCCACCACGAGUCU 299 250 272
AD-63973 A-127946 ACUCGUGGUGGACUUCUCUCA 84 A-127947 UGAGAGAAGTCCACCACGAGUCU 300 250 272
AD-63975 A-127915 ACUCGUGGUGGACUUCTCUCA 85 A-127906 UGAGAGAAGUCCACCACGAGUCU 301 250 272
AD-63976 A-127905 ACUCGUGGUGGACUUCUCUCA 86 A-127923 UGAGAGAAGUCCACCACGAGUCU 302 250 272
AD-63977 A-127917 ACUCGUGGUGGACUUCTCUCA 87 A-127931 UGAGAGAAGUCCACCACGAGUCU 303 250 272
AD-63978 A-127943 ACUCGUGGUGGACUUCUCUCA 88 A-127906 UGAGAGAAGUCCACCACGAGUCU 304 250 272
AD-63979 A-127908 ACUCGUGGUGGACUUCUCUCA 89 A-127906 UGAGAGAAGUCCACCACGAGUCU 305 250 272
AD-63980 A-127916 ACUCGUGGUGGACUUCTCUCA 90 A-127906 UGAGAGAAGUCCACCACGAGUCU 306 250 272
AD-63981 A-127905 ACUCGUGGUGGACUUCUCUCA 91 A-127924 UGAGAGAAGUCCACCACGAGUCU 307 250 272
AD-63982 A-127917 ACUCGUGGUGGACUUCTCUCA 92 A-127932 UGAGAGAAGUCCACCACGAGUCU 308 250 272
AD-63983 A-127944 ACUCGUGGUGGACUUCUCUCA 93 A-127940 UGAGAGAAGUCCACCACGAGUCU 309 250 272
AD-63985 A-127961 GUGGUGGACUUCUCUCAAUUU 94 A-127956 AAAUUGAGAGAAGUCCACCACGA 310 254 276
AD-63986 A-127969 GUGGUGGACUUCUCUCAAUUU 95 A-127956 AAAUUGAGAGAAGUCCACCACGA 311 254 276
AD-63987 A-127955 GUGGUGGACUUCUCUCAAUUU 96 A-127977 AAAUUGAGAGAAGUCCACCACGA 312 254 276
AD-63988 A-127986 UGGACUUCUCUCAAUUU 97 A-127987 AAAUUGAGAGAAGUCCACC 313 258_280
102
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3*) SEQ ID NO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-63989 A-127996 GUGGUGGACUUCUCUCAAUUU 98 A-127992 AAAUUGAGAGAAGUCCACCACGA 314 254 276
AD-63990 A-127950 GGUGGACUUCUCUCAAUUUUU 99 A-127951 AAAUUGAGAGAAGUCCACCUU 315 256 278
AD-63991 A-127962 GUGGUGGACUUCUCUCAAUUU 100 A-127956 AAAUUGAGAGAAGUCCACCACGA 316 254 276
AD-63992 A-127955 GUGGUGGACUUCUCUCAAUUU 101 A-127970 AAAUUGAGAGAAGUCCACCACGA 317 254 276
AD-63993 A-127955 GUGGUGGACUUCUCUCAAUUU 102 A-127978 AAAUUGAGAGAAGUCCACCACGA 318 254 276
AD-63994 A-127984 GGUGGACUUCUCUCAAUUU 103 A-127988 AAAUUGAGAGAAGUCCACCAC 319 256 278
AD-63995 A-127996 GUGGUGGACUUCUCUCAAUUU 104 A-127993 AAAUUGAGAGAAGUCCACCACGA 320 254 276
AD-63996 A-127952 GGUGGACUUCUCUCAAUUU 105 A-127953 AAAUUGAGAGAAGUCCACCUU 321 256 278
AD-63997 A-127963 GUGGUGGACUUCUCUCAAUUU 106 A-127956 AAAUUGAGAGAAGUCCACCACGA 322 254 276
AD-63999 A-127955 GUGGUGGACUUCUCUCAAUUU 107 A-127979 AAAUUGAGAGAAGUCCACCACGA 323 254 276
AD-64000 A-127986 UGGACUUCUCUCAAUUU 108 A-l 27989 AAAUUGAGAGAAGUCCACC 324 258 280
AD-64001 A-127996 GUGGUGGACUUCUCUCAAUUU 109 A-127994 AAAUUGAGAGAAGUCCACCACGA 325 254 276
AD-64002 A-127952 GGUGGACUUCUCUCAAUUU 110 A-127954 AAAUUGAGAGAAGUCCACCUU 326 256 278
AD-64003 A-127964 GUGGUGGACUUCUCUCAAUUU 111 A-127956 AAAUUGAGAGAAGUCCACCACGA 327 254 276
AD-64004 A-127955 GUGGUGGACUUCUCUCAAUUU 112 A-l 27972 AAAUUGAGAGAAGUCCACCACGA 328 254 276
AD-64005 A-127955 GUGGUGGACUUCUCUCAAUUU 113 A-127980 AAAUUGAGAGAAGUCCACCACGA 329 254 276
AD-64006 A-127990 GUGGUGGACUUCUCUCAAUUU 114 A-127991 AAAUUGAGAGAAGUCCACCACGA 330 254 276
AD-64007 A-127996 GUGGUGGACUUCUCUCAAUUU 115 A-127995 AAAUUGAGAGAAGUCCACCACGA 331 254 276
AD-64008 A-127955 GUGGUGGACUUCUCUCAAUUU 116 A-127956 AAAUUGAGAGAAGUCCACCACGA 332 254 276
AD-64008 A-127955 GUGGUGGACUUCUCUCAAUUU 117 A-127956 AAAUUGAGAGAAGUCCACCACGA 333 254 276
AD-64009 A-127965 GUGGUGGACUUCUCUCAAUUU 118 A-127956 AAAUUGAGAGAAGUCCACCACGA 334 254 276
AD-64010 A-127955 GUGGUGGACUUCUCUCAAUUU 119 A-127973 AAAUUGAGAGAAGUCCACCACGA 335 254 276
AD-64011 A-127955 GUGGUGGACUUCUCUCAAUUU 120 A-127981 AAAUUGAGAGAAGUCCACCACGA 336 254 276
AD-64012 A-127990 GUGGUGGACUUCUCUCAAUUU 121 A-127992 AAAUUGAGAGAAGUCCACCACGA 337 254 276
AD-64013 A-127997 GUGGUGGACTTCUCUCAAUUU 122 A-127998 AAAUUGAGAGAAGTCCACCACGA 338 254 276
AD-64014 A-127957 GUGGUGGACUUCUCUCAAUUU 123 A-127958 AAAUUGAGAGAAGUCCACCACGA 339 254 276
AD-64015 | A-127966 GUGGUGGACUUCUCUCAAUUU 124 A-127956 AAAUUGAGAGAAGUCCACCACGA 340 254_276
103
Duplex Naine Sense Oligo Name Sense Sequence (5’ to 3’) SEQ IDNO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-64016 A-127955 GUGGUGGACUUCUCUCAAUUU 125 A-127974 AAAUUGAGAGAAGUCCACCACGA 341 254 276
AD-64017 A-127968 GUGGUGGACUTCUCUCAAUUU 126 A-127982 AAAUUGAGAGAAGTCCACCACGA 342 254 276
AD-64018 A-127990 GUGGUGGACUUCUCUCAAUUU 127 A-127993 AAAUUGAGAGAAGUCCACCACGA 343 254 276
AD-64019 A-127959 GUGGUGGACUUCUCUCAAUUU 128 A-127956 AAAUUGAGAGAAGUCCACCACGA 344 254 276
AD-64020 A-127967 GUGGUGGACUUCUCUCAAUUU 129 A-127956 AAAUUGAGAGAAGUCCACCACGA 345 254 276
AD-64021 A-127955 GUGGUGGACUUCUCUCAAUUU 130 A-127975 AAAUUGAGAGAAGUCCACCACGA 346 254 276
AD-64022 A-127968 GUGGUGGACUTCUCUCAAUUU 131 A-127983 AAAUUGAGAGAAGTCCACCACGA 347 254 276
AD-64023 A-127990 GUGGUGGACUUCUCUCAAUUU 132 A-127994 AAAUUGAGAGAAGUCCACCACGA 348 254 276
AD-64024 A-127960 GUGGUGGACUUCUCUCAAUUU 133 A-127956 AAAUUGAGAGAAGUCCACCACGA 349 254 276
AD-64025 A-127968 GUGGUGGACUTCUCUCAAUUU 134 A-127956 AAAUUGAGAGAAGUCCACCACGA 350 254 276
AD-64026 A-127955 GUGGUGGACUUCUCUCAAUUU 135 A-127976 AAAUUGAGAGAAGUCCACCACGA 351 254 276
AD-64027 A-127984 GGUGGACUUCUCUCAAUUU 136 A-127985 AAAUUGAGAGAAGUCCACCAC 352 256 278
AD-64028 A-127990 GUGGUGGACUUCUCUCAAUUU 137 A-127995 AAAUUGAGAGAAGUCCACCACGA 353 254 276
AD-64272 A-128001 GUGCACUUCGCUUCACCUCUG 138 A-128002 CAGAGGUGAAGCGAAGUGCACAC 354 1577 1599
AD-64274 A-128363 GUUGACAAAAAUCCUCACAAU 139 A-128364 AUUGUGAGGAUUUUUGUCAACAA 355 215 237
AD-64275 A-128377 UGUUGACAAAAAUCCUCACAA 140 A-128378 UUGUGAGGAUUUUUGUCAACAAG 356 214 236
AD-64276 A-128393 GGUGGACUUCUCUCAAUUUUA 141 A-128394 UAAAAUUGAGAGAAGUCCACCAC 357 256 278
AD-64277 A-128407 UCUUUUGGAGUGUGGAUUCGA 142 A-128408 UCGAAUCCACACUCCAAAAGACA 358 2259 2281
AD-64277 A-128407 UCUUUUGGAGUGUGGAUUCGA 143 A-128408 UCGAAUCCACACUCCAAAAGACA 359 2259 2281
AD-64278 A-128423 ACUGUUCAAGCCUCCAAGCUA 144 A-128424 UAGCUUGGAGGCUUGAACAAGAC 360 1857 1879
AD-64279 A-128435 . UCUGCCGAUCCAUACUGCGGA 145 A-128436 UCCGCAGUAUGGAUCGGCAGAGG 361 1255 1277
AD-64280 A-128379 AUGUGUCUGCGGCGUUUUAUA 146 A-128380 UAUAAAACGCCGCAGACACAUCC 362 375 397
AD-64281 A-128395 CCCCGUCUGUGCCUUCUCAUA 147 A-128396 UAUGAGAAGGCACAGACGGGGAG 363 1545 1567
AD-64282 A-128409 GCCUAAUCAUCUCUUGUUCAU 148 A-128410 AUGAACAAGAGAUGAUUAGCGAG 364 1831 1853
AD-64283 A-128425 UCUAGACUCGUGGUGGACUUC 149 A-128426 GAAGUCCACCACGAGUCUAGACU 365 245 267
AD-64284 A-128437 CUGCCGAUCCAUACUGCGGAA 150 A-128438 UUCCGCAGUAUGGAUCGGCAGAG 366 1256 1278
AD-64285 A-128365 UUUUUCUUGUUGACAAAAAUA 151 A-128366 UAUUUUUGUCAACAAGAAAAACC 367 207_229
104
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-64286 A-128381 AUCUUCUUGUUGGUUCUUCUA 152 A-128382 UAGAAGAACCAACAAGAAGAUGA 368 426 448
AD-64289 A-128367 GUUUUUCUUGUUGACAAAAAU 153 A-128368 AUUUUUGUCAACAAGAAAAACCC 369 206 228
AD-64290 A-128383 CUGCCUAAUCAUCUCUUGUUA 154 A-128384 UAACAAGAGAUGAUUAGGCAGAG 370 1829 1851
AD-64291 A-128399 UCCUCACAAUACCACAGAGUA 155 A-128400 UACUCUGUGGUAUUGUGAGGAUU 371 226 248
AD-64292 A-128413 CUUGUUGACAAAAAUCCUCAA 156 A-128414 UUGAGGAUUUUUGUCAACAAGAA 372 212 234
AD-64293 A-128439 GCAACUUUUUCACCUCUGCCU 157 A-128440 AGGCAGAGGUGAAAAAGUUGCAU 373 1814 1836
AD-64294 A-128369 GGGAACAAGAGCUACAGCAUA 158 A-128370 UAUGCUGUAGCUCUUGUUCCCAA 374 2828 2850
AD-64295 A-128385 CGUGGUGGACUUCUCUCAAUU 159 A-128386 AAUUGAGAGAAGUCCACCAGCAG 375 253 275
AD-64297 A-128415 CUGCUGCUAUGCCUCAUCUUA 160 A-128416 UAAGAUGAGGCAUAGCAGCAGGA 376 411 433
AD-64298 A-128427 GUUGGAUGUGUCUGCGGCGUU 161 A-128428 AACGCCGCAGACACAUCCAACGA 377 370 392
AD-64299 A-128441 UUCAUCCUGCUGCUAUGCCUA 162 A-128442 UAGGCAUAGCAGCAGGAUGAAGA 378 405 427 ·
AD-64300 A-128371 UUCUUGUUGACAAAAAUCCUA 163 A-128372 UAGGAUUUUUGUCAACAAGAAAA 379 210 232
AD-64302 A-128417 UAUAUGGAUGAUGUGGUAUUA 164 A-128418 UAAUACCACAUCAUCCAUAUAAC 380 734 756
AD-64303 A-l 28429 UUCAUCCUGCUGCUAUGCCUC 165 A-128430 GAGGCAUAGCAGCAGGAUGAAGA 381 405 427
AD-64304 A-128443 GUGCACUUCGCUUCACCUCUA 166 A-128444 UAGAGGUGAAGCGAAGUGCACAC 382 1577 1599
AD-64305 A-128373 UUGACAAAAAUCCUCACAAUA 167 A-128374 UAUUGUGAGGAUUUUUGUCAACA 383 216 238
AD-64307 A-128403 AAGCCUCCAAGCUGUGCCUUA 168 A-128404 UAAGGCACAGCUUGGAGGCUUGA 384 1864 1886
AD-64308 A-128419 CCUCUUCAUCCUGCUGCUAUA 169 A-128420 UAUAGCAGCAGGAUGAAGAGGAA 385 401 423
AD-64309 A-128431 CCUGCUGCUAUGCCUCAUCUU 170 A-128432 AAGAUGAGGCAUAGCAGCAGGAU 386 410 432
AD-64310 A-128375 CAUCUUCUUGUUGGUUCUUCU 171 A-128376 AGAAGAACCAACAAGAAGAUGAG 387 425 447
AD-64311 A-128391 CCGUCUGUGCCUUCUCAUCUA 172 A-l 28392 UAGAUGAGAAGGCACAGACGGGG 388 1547 1569
AD-64312 A-128405 CCUCAUCUUCUUGUUGGUUCU 173 A-128406 AGAACCAACAAGAAGAUGAGGCA 389 422 444
AD-64313 A-128421 CCACCAAAUGCCCCUAUCUUA 174 A-128422 UAAGAUAGGGGCAUUUGGUGGUC 390 2298 2320
AD-64314 A-128433 GCUCCUCUGCCGAUCCAUACU 175 A-128434 AGUAUGGAUCGGCAGAGGAGCCA 391 1250 1272
AD-64315 A-128363 GUUGACAAAAAUCCUCACAAU 176 A-128445 AUUGUGAGGAUUUUUGUCAACAA 392 215 237
AD-64316 A-128377 UGUUGACAAAAAUCCUCACAA 177 A-128453 UUGUGAGGAUUUUUGUCAACAAG 393 214 236
AD-64317 A-128393 GGUGGACUUCUCUCAAUUUUA 178 A-128461 UAAAAUUGAGAGAAGUCCACCAC 394 256_278
105
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-64318 A-128407 UCUUUUGGAGUGUGGAUUCGA 179 A-128469 UCGAAUCCACACUCCAAAAGACA 395 2259_2281
AD-64318 A-128407 UCUUUUGGAGUGUGGAUUCGA 180 A-128469 UCGAAUCCACACUCCAAAAGACA 396 2259_2281
AD-64319 A-128423 ACUGUUCAAGCCUCCAAGCUA 181 A-128477 UAGCUUGGAGGCUUGAACAAGAC 397 1857_1879
AD-64320 A-128435 UCUGCCGAUCCAUACUGCGGA 182 A-128483 UCCGCAGUAUGGAUCGGCAGAGG 398 1255_1277
AD-64321 A-123463 AGUUAUAUGGAUGAUGUGGUA 183 A-128446 UACCACAUCAUCCAUAUAACUGA 399 731_753
AD-64322 A-128379 AUGUGUCUGCGGCGUUUUAUA 184 A-128454 UAUAAAACGCCGCAGACACAUCC 400 375_397
AD-64323 A-128395 CCCCGUCUGUGCCUUCUCAUA 185 A-128462 UAUGAGAAGGCACAGACGGGGAG 401 1545_1567
AD-64324 A-128409 GCCUAAUCAUCUCUUGUUCAU 186 A-128470 AUGAACAAGAGAUGAUUAGCGAG 402 1831_1853
AD-64325 A-128425 UCUAGACUCGUGGUGGACUUC 187 A-128478 GAAGUCCACCACGAGUCUAGACU 403 245_267
AD-64326 A-128437 CUGCCGAUCCAUACUGCGGAA 188 A-128484 UUCCGCAGUAUGGAUCGGCAGAG 404 1256_1278
AD-64328 A-128381 AUCUUCUUGUUGGUUCUUCUA 189 A-128455 UAGAAGAACCAACAAGAAGAUGA 405 426_448
AD-64330 A-128411 UUCUCUCAAUUUUCUAGGGGA 190 A-128471 UCCCCUAGAAAAUUGAGAGAAGU 406 263_285
AD-64331 A-127905 ACUCGUGGUGGACUUCUCUCA 191 A-127907 UGAGAGAAGUCCACCACGAGUCU 407 250_272
AD-64332 A-128001 GUGCACUUCGCUUCACCUCUG 192 A-128485 CAGAGGUGAAGCGAAGUGCACAC 408 1577_1599
AD-64333 A-128367 GUUUUUCUUGUUGACAAAAAU 193 A-128448 AUUUUUGUCAACAAGAAAAACCC 409 206 228
AD-64334 A-128383 CUGCCUAAUCAUCUCUUGUUA 194 A-128456 UAACAAGAGAUGAUUAGGCAGAG 410 18291851
AD-64335 A-128399 UCCUCACAAUACCACAGAGUA 195 A-128464 UACUCUGUGGUAUUGUGAGGAUU 411 226_248
AD-64336 A-128413 CUUGUUGACAAAAAUCCUCAA 196 A-128472 UUGAGGAUUUUUGUCAACAAGAA 412 212_234
AD-64337 A-127955 GUGGUGGACUUCUCUCAAUUU 197 A-127958 AAAUUGAGAGAAGUCCACCACGA 413 254_276
AD-64338 A-128439 GCAACUUUUUCACCUCUGCCU 198 A-128486 AGGCAGAGGUGAAAAAGUUGCAU 414 1814_1836
AD-64339 A-128369 GGGAACAAGAGCUACAGCAUA 199 A-128449 UAUGCUGUAGCUCUUGUUCCCAA 415 28282850
AD-64341 A-l28401 UCAUCUUCUUGUUGGUUCUUA 200 A-128465 UAAGAACCAACAAGAAGAUGAGG 416 424_446
AD-64342 A-128415 CUGCUGCUAUGCCUCAUCUUA 201 A-128473 UAAGAUGAGGCAUAGCAGCAGGA 417 411433
AD-64343 A-128427 GUUGGAUGUGUCUGCGGCGUU 202 A-128479 AACGCCGCAGACACAUCCAACGA 418 370_392
AD-64344 A-128441 UUCAUCCUGCUGCUAUGCCUA 203 A-128487 UAGGCAUAGCAGCAGGAUGAAGA 419 405_427
AD-64345 A-128371 UUCUUGUUGACAAAAAUCCUA 204 A-128450 UAGGAUUUUUGUCAACAAGAAAA 420 210_232
AD-64347 A-123487 GGAUGUGUCUGCGGCGUUUUA 205 A-128466 UAAAACGCCGCAGACACAUCCAG 421 373_395
106
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ IDNO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-64348 A-128417 UAUAUGGAUGAUGUGGUAUUA 206 A-128474 UAAUACCACAUCAUCCAUAUAAC 422 734 756
AD-64349 A-128429 UUCAUCCUGCUGCUAUGCCUC 207 A-128480 GAGGCAUAGCAGCAGGAUGAAGA 423 405 427
AD-64350 A-128443 GUGCACUUCGCUUCACCUCUA 208 A-128488 UAGAGGUGAAGCGAAGUGCACAC 424 1577 1599
AD-64351 A-128373 UUGACAAAAAÜCCUCACAAUA 209 A-128451 UAUUGUGAGGAUUUUUGUCAACA 425 216 238
AD-64352 A-128389 CCAAGUGUUUGCUGACGCAAA 210 A-128459 UUUGCGUCAGCAAACACUUGGCA 426 1174 1196
AD-64352 A-128389 CCAAGUGUUUGCUGACGCAAA 211 A-128459 UUUGCGUCAGCAAACACUUGGCA 427 1174 1196
AD-64353 A-128403 AAGCCUCCAAGCUGUGCCUUA 212 A-128467 UAAGGCACAGCUUGGAGGCUUGA 428 1864 1886
AD-64354 A-128419 CCUCUUCAUCCUGCUGCUAUA 213 A-128475 UAUAGCAGCAGGAUGAAGAGGAA 429 401 423
AD-64355 A-128431 CCUGCUGCUAUGCCUCAUCUU 214 A-128481 AAGAUGAGGCAUAGCAGCAGGAU 430 410 432
AD-64356 A-128375 CAUCUUCUUGUUGGUUCUUCU 215 A-128452 AGAAGAACCAACAAGAAGAUGAG 431 425 447
AD-64357 A-128391 CCGUCUGUGCCUUCUCAUCUA 216 A-128460 UAGAUGAGAAGGCACAGACGGGG 432 1547 1569
AD-64358 A-128405 CCUCAUCUUCUUGUUGGUUCU 217 A-128468 AGAACCAACAAGAAGAUGAGGCA 433 422 444
AD-64359 A-128421 CCACCAAAUGCCCCUAUCUUA 218 A-128476 UAAGAUAGGGGCAUUUGGUGGUC 434 2298_2320
AD-64360 A-128433 GCUCCUCUGCCGAUCCAUACU 219 A-128482 AGUAUGGAUCGGCAGAGGAGCCA 435 1250 1272
AD-64700 A-129379 ACUCGUGGUGTACUUCUCUCA 220 A-127906 UGAGAGAAGUCCACCACGAGUCU 436 250 272
AD-64701 A-127905 ACUCGUGGUGGACUUCUCUCA 221 A-l 29387 UGAGAGAAGTCCACCACGAGUCU 437 250 272
AD-64702 A-127905 ACUCGUGGUGGACUUCUCUCA 222 A-129395 UGAGAGAAGUCCACCACGAGUCU 438 250 272
AD-64703 A-129376 ACUCGUGGUGGACUUCACUCA 223 A-129385 UGAGAGAAGTCCACCACGAGUCU 439 250 272
AD-64704 A-129381 ACUCGUGGTGTACUUCACUCA 224 A-129389 UGAGAGAAGUCCACCACGAGUCU 440 250 272
AD-64705 A-129380 ACUCGUGGUGTACUUCACUCA 225 A-127906 UGAGAGAAGUCCACCACGAGUCU 441 250 272
AD-64706 A-127905 ACUCGUGGUGGACUUCUCUCA 226 A-129388 UGAGAGAAGUCCACCACGAGUCU 442 250 272
AD-64707 A-127905 ACUCGUGGUGGACUUCUCUCA 227 A-129396 UGAGAGAAGTCCACCACGAGUCU 443 250 272
AD-64708 A-129382 ACUCGUGGTGGACUUCTCUCA 228 A-129385 UGAGAGAAGTCCACCACGAGUCU 444 250 272
AD-64709 A-129373 ACUCGUGGUGGACUUCUCUCA 229 A-129391 UGAGAGAAGTCCACCACGAGUCU 445 250 272
AD-64710 A-129373 ACUCGUGGUGGACUUCUCUCA 230 A-127906 UGAGAGAAGUCCACCACGAGUCU 446 250 272
AD-64711 A-129381 ACUCGUGGTGTACUUCACUCA 231 A-127906 UGAGAGAAGUCCACCACGAGUCU 447 250 272
AD-64712 A-127905 ACUCGUGGUGGACUUCUCUCA 232 A-129389 UGAGAGAAGUCCACCACGAGUCU 448 250_272
107
Duplex Name Sensc Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-64713 A-127905 ACUCGUGGUGGACUUCUCUCA 233 A-129397 UGAGAGAAGTCCACCACGAGUCU 449 250 272
AD-64714 A-129384 ACUCGUGGTGGACUUCACUCA 234 A-129385 UGAGAGAAGTCCACCACGAGUCU 450 250 272
AD-64715 A-129376 ACUCGUGGUGGACUUCACUCA 235 A-129391 UGAGAGAAGTCCACCACGAGUCU 451 250 272
AD-64716 A-129374 ACUCGUGGUGGACUUCUCUCA 236 A-127906 UGAGAGAAGUCCACCACGAGUCU 452 250 272
AD-64717 A-129382 ACUCGUGGTGGACUUCTCUCA 237 A-127906 UGAGAGAAGUCCACCACGAGUCU 453 250 272
AD-64718 A-127905 ACUCGUGGUGGACUUCUCUCA 238 A-129390 UGAGAGAAGUCCACCACGAGUCU 454 250 272
AD-64719 A-127917 ACUCGUGGUGGACUUCTCUCA 239 A-129385 UGAGAGAAGTCCACCACGAGUCU 455 250 272
AD-64720 A-129381 ACUCGUGGTGTACUUCACUCA 240 A-129385 UGAGAGAAGTCCACCACGAGUCU 456 250 272
AD-64721 A-129382 ACUCGUGGTGGACUUCTCUCA 241 A-129391 UGAGAGAAGTCCACCACGAGUCU 457 250 272
AD-64722 A-129375 ACUCGUGGUGGACUUCCUCA 242 A-127906 UGAGAGAAGUCCACCACGAGUCU 458 250 272
AD-64723 A-129383 ACUCGUGGUGGACUUCTCUCA 243 A-127906 UGAGAGAAGUCCACCACGAGUCU 459 250_272
AD-64725 A-127917 ACUCGUGGUGGACUUCTCUCA 244 A-129398 UGAGAGAAGTCCACCACGAGUCU 460 250_272
AD-64726 A-129373 ACUCGUGGUGGACUUCUCUCA 245 A-129389 UGAGAGAAGUCCACCACGAGUCU 461 250 272
AD-64727 A-129384 ACUCGUGGTGGACUUCACUCA 246 A-129391 UGAGAGAAGTCCACCACGAGUCU 462 250 272
AD-64728 A-129376 ACUCGUGGUGGACUUCACUCA 247 A-127906 UGAGAGAAGUCCACCACGAGUCU 463 250 272
AD-64729 A-129384 ; ACUCGUGGTGGACUUCACUCA 248 A-127906 UGAGAGAAGUCCACCACGAGUCU 464 250 272
AD-64730 A-127905 ACUCGUGGUGGACUUCUCUCA 249 A-129392 UGAGAGAAGTCCACCACGAGUCU 465 250 272
AD-64731 A-129399 ACUCGUGGUGGACUUCTCUCA 250 A-129385 UGAGAGAAGTCCACCACGAGUCU 466 250_272
AD-64732 A-129376 ACUCGUGGUGGACUUCACUCA 251 A-129389 UGAGAGAAGUCCACCACGAGUCU 467 250_272
AD-64733 A-129381 ACUCGUGGTGTACUUCACUCA 252 A-129391 UGAGAGAAGTCCACCACGAGUCU 468 250 272
AD-64734 A-129377 ACUCGUGGUGGACUUCCCUCA 253 A-127906 UGAGAGAAGUCCACCACGAGUCU 469 250_272
AD-64735 A-127905 ACUCGUGGUGGACUUCUCUCA 254 A-129385 UGAGAGAAGTCCACCACGAGUCU 470 250 272
AD-64736 A-127905 ACUCGUGGUGGACUUCUCUCA 255 A-129393 UGAGAGAAGTCCACCACGAGUCU 471 250_272
AD-64737 A-129399 ACUCGUGGUGGACUUCTCUCA 256 A-129398 UGAGAGAAGTCCACCACGAGUCU 472 250 272
AD-64738 A-129382 ACUCGUGGTGGACUUCTCUCA 257 A-129389 UGAGAGAAGUCCACCACGAGUCU 473 250 272
AD-64739 A-129378 ACUCGUGGUGGACUUCCCUCA 258 A-127906 UGAGAGAAGUCCACCACGAGUCU 474 250 272
AD-64740 A-127905 ACUCGUGGUGGACUUCUCUCA 259 A-129386 UGAGAGAAGTCCACCACGAGUCU 475 250_272
108 Ο
Duplex Namc Sense Oligo Name Sense Sequence (5’ to 3’) SEQ IDNO Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO: Position in NC 003977.1
AD-64741 A-127905 ACUCGUGGUGGACUUCUCUCA 260 A-129394 UGAGAGAAGTCCACCACGAGUCU 476 250_272
AD-64742 A-129373 ACUCGUGGUGGACUUCUCUCA 261 A-129385 UGAGAGAAGTCCACCACGAGUCU 477 250_272
AD-64743 A-129384 ACUCGUGGTGGACUUCACUCA 262 A-129389 UGAGAGAAGUCCACCACGAGUCU 478 250 272
Table 3. Exemplary Modified Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-61522 A-123463 AfsgsUfuAfuAfuGfGfAfijGfaUfgUfgGfiiAfL96 479 A-123464 usAfscCfaCfaUfcAfuccAfiiAfuAfaCfusgsa 694
AD-61547 A-123487 GfsgsAfiiGfiiGfiiCfUfGfcGfgCfgUfuUfuAfL96 480 A-123488 usAfsaAfaCfgCfcGfcagAfcAfcAfuCfcsasg 695
AD-63938 A-127896 Y44ACUCGUGGUGGACUUCUCUCA 481 A-127897 UGAGAGAAGUCCACCACGAGUCU 696
AD-63939 A-127909 ascsucGfuGfgUfGfGfaCfiiucUfcucaL96 482 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 697
AD-63940 A-127917 ascsucguggugdGacuuc(Tgn)cucaL96 483 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 698
AD-63941 A-127905 AfscsUfcGfuGfgUfGfGfaCfiiUfcUfcUfcAfL96 484 A-127925 usGfsaGfagaAfguccaCfcAfcgaGftiscsu 699
AD-63942 A-127933 uscsGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 485 A-127934 usGfsaGfaGfaAfgUfccaCfcAfcGfasgsu 700
AD-63943 A-127944 ascsucGfuGfguGfGfaCftiucucucaL96 486 A-127942 usGfsAfgaGfaAfgUfccaCfcAfcGfaguscsu 701
AD-63945 A-127910 ascsucguGfgUfGfGfaCftiucUfcucaL96 487 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 702
AD-63946 A-127918 ascsucguGfgUfGfGfacuuCfucucaL96 488 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 703
AD-63947 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 489 A-127926 usGfsaGfagaagUfccaCfcAfcgaGfuscsu 704
AD-63948 A-127935 gsusGfgUfGfGfaCfuUfcUfcUfcAfL96 490 A-127936 usGfsaGfaGfaAfgUfccaCfcAfcsgsa 705
AD-63949 A-127944 ascsucGfuGfguGfGfaCfiiucucucaL96 491 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 706
AD-63950 A-127900 Y44UfcGfuGfgUfgGfaCfuUfcUfcUfcAfiisuY44 492 A-127901 usGfsasGfaGfaAfgUfcCfaCfcAfcGfausu 707
AD-63951 A-127911 ascsucguGfgUfGfGfaCfuucucucaL96 493 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 708
AD-63952 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 494 A-127919 usGfsaGfaGfaagUfccaCfcAfcGfaGfuscsu 709
AD-63953 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 495 A-127927 usGfsagagaAfgUfccaCfcAfcgaguscsu 710
Duplex Namc Sense Oligo Namc Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-63955 A-127945 ascsucgugguGfGfacuucucucaL96 496 A-127940 usGfsAfgAfgAfaGfiiccaCfCfaCfgAfguscsu 711
AD-63956 A-127902 Y44uscsGfuGfgUfgGfaCfuUfcUfcUfcAfY44 497 A-127903 usGfsaGfaGfaAfgUfcCfaCfcAfcGfasusu 712
AD-63957 A-127912 ascsucguGfgUfGfGfacuucucucaL96 498 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 713
AD-63958 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 499 A-127920 usGfsagaGfaAfgUfccaCfcAfcgaGfuscsu 714
AD-63959 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 500 A-127928 usGfsaGfagaAfguccaCfcAfcgaguscsu 715
AD-63960 A-126619 usasUfuUfCfCfiiAfgGfgUfaCfaAfL96 501 A-127938 PusGfsaGfaGfaAfgUfccaCfcAfcsgsa 716
AD-63961 A-127945 ascsucgugguGfGfacuucucucaL96 502 A-127942 usGfsAfgaGfaAfgUfccaCfcAfcGfaguscsu 717
AD-63962 A-127902 Y44uscsGfuGfgUfgGfaCfiiUfcUfcUfcAfY44 503 A-127904 PusGfsaGfaGfaAfgUfcCfaCfcAfcGfasusu 718
AD-63963 A-127913 ascsucguggUfgGfacuucucucaL96 504 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 719
AD-63964 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 505 A-127921 usGfsaGfaGfaAfgUfccaCfcAfcgaguscsu 720
AD-63965 A-127905 AfscsUfcGfuGfgUfGfGfaCfiiUfcUfcUfcAfL96 506 A-127929 usGfsagaGfaaGfuccaCfcAfcgaguscsu 721
AD-63966 A-127939 ascsUfcGfiigguGfGfaCfiiuCfuCfucaL96 507 A-127940 usGfsAfgAfgAfaGfticcaCfCfaCfgAfguscsu 722
AD-63967 A-127945 ascsucgugguGfGfacuucucucaL96 508 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 723
AD-63968 A-127905 AfscsUfcGfuGfgUfGfGfaCfiiUfcUfcUfcAfL96 509 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 724
AD-63968 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 510 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 725
AD-63968 A-127905 AfscsUfcGfiiGfgUfGfGfaCfiiUfcUfcUfcAfL96 511 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 726
AD-63969 A-127914 ascsucguggugGfacuucucucaL96 512 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 727
AD-63970 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 513 A-127922 usGfsagaGfaagUfccaCfcAfcgaGfiiscsu 728
AD-63971 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAiL96 514 A-127930 usGfsagaGfaaguccaCfcAfcgaguscsu 729
AD-63972 A-127941 ascsUfcGftiGfguGfGfaCfiiuCfiiCfiicaL96 515 A-127942 usGfsAfgaGfaAfgUfccaCfcAfcGfaguscsu 730
AD-63973 A-127946 ascsucguggudGdGacuucucucaL96 516 A-127947 usdGsaGfaGfaAfgdTccadCcAfcGfaguscsu 731
AD-63975 A-127915 ascsucguggUfgGfacuuc(Tgn)cucaL96 517 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 732
AD-63976 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 518 A-127923 usGfsagaGfaAfgUfccaCfcAfcgaguscsu 733
AD-63977 A-127917 ascsucguggugdGacuuc(Tgn)cucaL96 519 A-127931 usdGsagagaaguccadCcacgaguscsu 734
AD-63978 A-127943 ascsUfcGfuGfguGfGfaCfuUfcUfcUfcaL96 520 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 735
AD-63979 A-127908 ascsucGfuGfgUfGfGfaCfiiucUfcucAfL96 521 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 736
110
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-63980 A-127916 ascsucguggugGfacuuc(Tgn)cucaL96 522 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 737
AD-63981 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 523 A-127924 usGfsaGfagaAfgUfccaCfcAfcgaGfuscsu 738
AD-63982 A-127917 ascsucguggugdGacuuc(Tgn)cucaL96 524 A-127932 PusdGsagagaaguccadCcacgaguscsu 739
AD-63983 A-127944 ascsucGfuGfguGfGfaCfiiucucucaL96 525 A-127940 usGfsAfgAfgAfaGfuccaCfCfaCfgAfguscsu 740
AD-63985 A-127961 gsusggugGfaCfUfUfcUfcucAfauuuL96 526 A-127956 asAfsaUfiiGfaGfaGfaagUfcCfaCfcAfcsgsa 741
AD-63986 A-127969 gsusggugGfaCiUfUfcucuCfaauuuL96 527 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 742
AD-63987 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 528 A-127977 asAfsaUfugagaGfaagUfcCfaccAfcsgsa 743
AD-63988 A-127986 usgsGfaCfUfUfcUfcUfcAfaUfuUfL96 529 A-127987 asAfsaUftiGfaGfaGfaagUfcCfascsc 744
AD-63989 A-127996 gsusgguggacUfUfcucucaauuuL96 530 A-127992 asAfsAfUfuGfaGfaGfaagUfcCfaCfcacsgsa 745
AD-63990 A-127950 Y44GfgUfgGfaCfiiUfcUfcUfcAfaUfuUfusuY44 531 A-127951 as AfsasU fiiGfaGfaGfa AfgU fcCfaCfcusu 746
AD-63991 A-127962 gsusggugGfaCfUfUfcUfcucaauuuL96 532 A-127956 as AfsaU fuGfaGfaGfaagU fcCfaCfc Afcsgsa 747
AD-63992 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 533 A-127970 asAfsaUfiiGfagaGfaagUfcCfaCfcAfcsgsa 748
AD-63993 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfiiUfL96 534 A-127978 asAfsauugaGfaGfaagUfcCfaccacsgsa 749
AD-63994 A-127984 gsgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 535 A-127988 PasAfsaUfuGfaGfaGfaagUfcCfaCfcsasc 750
AD-63995 A-127996 gsusgguggacUfUfcucucaauuuL96 536 A-127993 asAfsAfuuGfaGfaGfaagUfiCfcaCfcacsgsa 751
AD-63996 A-127952 Y44gsgsUfgGfaCftiUfcUfcUfcAfaUfuUfY44 537 A-127953 asAfsaUfuGfaGfaGfaAfgUfcCfaCfcsusu 752
AD-63997 A-127963 gsusggugGfaCfUfUfcucucaauuuL96 538 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 753
AD-63999 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfiiUfL96 539 A-127979 asAfsaUfiigaGfagaagUfcCfaccacsgsa 754
AD-64000 A-127986 usgsGfaCfUfUfcUfcUfcAfaUfuUfL96 540 A-127989 PasAfsaUfuGfaGfaGfaagUfcCfascsc 755
AD-64001 A-127996 gsusgguggacUfüfcucucaauuuL96 541 A-127994 asAfsAfUfuGfaGfaGfaagUfCfcaCfcacsgsa 756
AD-64002 A-127952 Y44gsgsUfgGfaCfiiUfcUfcUfcAfaUfiiUfY44 542 A-127954 PasAfsaUfuGfaGfaGfaAfgUfcCfaCfcsusu 757
AD-64003 A-127964 gsusgguggaCfuUfcucucaauuuL96 543 A-127956 asAfsaUfiiGfaGfaGfaagUfcCfaCfcAfcsgsa 758
AD-64004 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 544 A-127972 asAfsaUfuGfaGfaGfaagUfcCfaccacsgsa 759
AD-64005 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 545 A-127980 · asAfsauuGfagAfgaagUfcCfaccacsgsa 760
AD-64006 Λ-127990 gsusGfgugGfaCfUfUfcUfcUfcAfaUfuuL96 546 A-127991 asAfsaUfiiGfaGfaGfaagUfcCfaCfcacsgsa 761
AD-64007 A-127996 gsusgguggacUfUfcucucaauuuL96 547 A-127995 asAfsAfUftigaGfaGfaagUfCfcaCfcacsgsa 762
111
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-64008 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 548 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 763
AD-64008 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 549 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 764
AD-64009 A-127965 gsusgguggacuUfcucucaauuuL96 550 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 765
AD-64010 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 551 A-127973 asAfsauuGfagaGfaagUfcCfaccAfcsgsa 766
AD-64011 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 552 A-127981 asAfsauuGfagagaagUfcCfaccacsgsa 767
AD-64012 A-127990 gsusGfgugGfaCfUfUfcUfcUfcAfaUfuuL96 553 A-127992 asAfsAfUfuGfaGfaGfaagUfcCfaCfcacsgsa 768
AD-64013 A-127997 gsusgguggacdTdTcucucaauuuL96 554 A-127998 asdAsAftiugaGfaGfaagdTdCcaCfcacsgsa 769
AD-64014 A-127957 Y44GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfiiUfL96 555 A-l 27958 PasAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 770
AD-64015 A-127966 gsusgguggaCfiiUfcucuc(Agn)auuuL96 556 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 771
AD-64016 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 557 A-127974 asAfsauuGfaGfaGfaagUfcCfaccacsgsa 772
AD-64017 A-127968 gsusgguggacudTcucuc(Agn)auuuL96 558 A-127982 asdAsauugagagaagdTccaccacsgsa 773
AD-64018 A-127990 gsusGfgugGfaCfUfUfcUfcUfcAfaUfuuL96 559 A-127993 asAfsAfuuGfaGfaGfaagUfCfcaCfcacsgsa 774
AD-64019 A-127959 gsusggUfgGfaCfUfUfcUfcucAfauuUfL96 560 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 775
AD-64020 A-127967 gsusgguggacuUfcucuc(Agn)auuuL96 561 A-127956 asAfsaUfiiGfaGfaGfaagUfcCfaCfcAfcsgsa 776
AD-64021 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 562 A-127975 asAfsaUfiigaGfaGfaagUfcCfaccAfcsgsa 777
AD-64022 A-127968 gsusgguggacudTcucuc(Agn)auuuL96 563 A-127983 PasdAsauugagagaagdTccaccacsgsa 778
AD-64023 A-127990 gsusGfgugGfaCf(JfUfcUfcUfcAfaUfuuL96 564 A-l 27994 asAfsAfUftiGfaGfaGfaagUfCfcaCfcacsgsa 779
AD-64024 A-127960 gsusggUfgGfaCfUfUfcUfcucAfauuuL96 565 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 780
AD-64025 A-127968 gsusgguggacudTcucuc(Agn)auuuL96 566 A-127956 asAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 781
AD-64026 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 567 A-127976 asAfsallfugaGfagaagUfcCfaccAfcsgsa 782
AD-64027 A-127984 gsgUfgGfaCfUfUfcUfcUfcAfaUfiiUfL96 568 A-127985 asAfsallfiiGfaGfaGfaagUfcCfaCfcsasc 783
AD-64028 A-127990 gsusGfgugGfaCfUfUfcUfcUfcAfaUfuuL96 569 A-127995 asAfsAfUfugaGfaGfaagUfCfcaCfcacsgsa 784
AD-64272 A-128001 GfsusGfcAfcUfiiCfGfCfuUfcAfcCfuCfuGfL96 570 A-128002 csAfsgAfgGfuGfaAfgcgAfaGfuGfcAfcsasc 785
AD-64274 A-128363 GfsusUfgAfcAfaAfAfAfuCfcUfcAfcAfaUfL96 571 A-128364 asUfsuGfiiGfaGfgAfuuuUfuGfuCfaAfcsasa 786
AD-64275 A-128377 UfsgsUfùGfaCfaAfAfAfaUfcCfuCfaCfaAfL96 572 A-128378 usUfsgUfgAfgGfaUfuuuUfgUfcAfaCfasasg 787
AD-64276 A-128393 GfsgsUfgGfaCfuUfCfUfcUfcAfaUfuUfuAfL96 573 A-128394 usAfsaAfaUfuGfaGfagaAfgUfcCfaCfcsasc 788
112
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-64277 A-128407 UfscsUfuUfuGfgAfGfUfgUfgGfaUfuCfgAfL96 574 A-128408 usCfsgAfaUfcCfaCfacuCfcAfaAfaGfascsa 789
AD-64277 A-128407 UfscsUfuUfuGfgAfGfUfgUfgGfaUfuCfgAfL96 ' 575 A-128408 usCfsgAfaUfcCfaCfacuCfcAfaAfaGfascsa 790
AD-64278 A-128423 AfscsUfgUfuCfaAfGfCfcUfcCfaAfgCfuAfL96 576 A-128424 usAfsgCfuUfgGfaGfgcuUfgAfaCfaAfgsasc 791
AD-64279 A-128435 UfscsUfgCfcGfaUfCfCfaUfaCfiiGfcGfgAfL96 577 A-128436 usCfscGfcAfgUfaUfggaUfcGfgCfaGfasgsg 792
AD-64280 A-128379 AfsusGfuGfuCftiGfCfGfgCfgUfuUfuAfuAfL96 578 A-128380 usAfsuAfaAfaCfgCfcgcAfgAfcAfcAfuscsc 793
AD-64281 A-128395 CfscsCfcGftiCfuGfUfGfcCfuUfcUfcAfuAfL96 579 A-128396 usAfsuGfaGfaAfgGfcacAfgAfcGfgGfgsasg 794
AD-64282 A-128409 GfscsCfuAfaUfcAfUfCfuCfuUfgUfuCfaUfL96 580 A-128410 asUfsgAfaCfaAfgAfgauGfaUfuAfgCfgsasg 795
AD-64283 A-128425 UfscsUfaGfaCfuCfGfUfgGftiGfgAfcUfuCfL96 581 A-128426 gsAfsaGfuCfcAfcCfacgAfgUfcUfaGfascsu 796
AD-64284 A-128437 CfsusGfcCfgAfuCfCfAftiAfcUfgCfgGfaAfL96 582 A-128438 usUfscCfgCfaGfuAfiiggAfuCfgGfcAfgsasg 797
AD-64285 A-128365 UfsusUfuUfcUfuGfUfUfgAfcAfaAfaAfiiAfL96 583 A-128366 usAfsuUfuUfuGfuCfaacAfaGfaAfaAfascsc 798
AD-64286 A-128381 AfsusCfuUfcUftiGfUfUfgGfiiUfcUfuCfuAfL96 584 A-128382 usAfsgAfaGfaAfcCfaacAfaGfaAfgAfiisgsa 799
AD-64289 A-128367 GfsusUfuUfuCfuUfGfUfuGfaCfaAfaAfaUfL96 585 A-128368 asU fsuU fiiU fgU fc AfacaAfg AfaAfaAfcscsc 800
AD-64290 A-128383 CfsusGfcCfuAfaUfCfAfuCfuCfuUfgUfuAfL96 586 A-128384 usAfsaCfaAfgAfgAfugaUfuAfgGfcAfgsasg 801
AD-64291 A-128399 UfscsCfiiCfaCfaAfUfAfcCfaCfaGfaGfuAfL96 587 A-128400 usAfscUfcUfgUfgGfiiauUfgUfgAfgGfasusu 802
AD-64292 A-128413 CfsusUfgUfuGfaCfAfAfaAfaUfcCfuCfaAfL96 588 A-128414 usUfsgAfgGfaUfuUfuugUfcAfaCfaAfgsasa 803
AD-64293 A-128439 GfscsAfaCfuUfuUfUfCfaCfcUfcUfgCfcUfL96 589 A-128440 asGfsgCfaGfaGfgUfgaaAfaAfgUfuGfcsasu 804
AD-64294 A-128369 GfsgsGfaAfcAfaGfAfGfcUfaCfaGfcAfuAfL96 590 A-128370 usAfsuGfcUfgUfaGfcucUfuGftiUfcCfcsasa 805
AD-64295 A-128385 CfsgsUfgGfuGfgAfCfUfuCfuCfuCfaAfuUfL96 591 A-128386 asAfsuUfgAfgAfgAfaguCfcAfcCfaGfcsasg 806
AD-64297 A-128415 CfsusGfcUfgCftiAfUfGfcCfiiCfaUfcUfuAfL96 592 A-128416 usAfsaGfaUfgAfgGfcauAfgCfaGfcAfgsgsa 807
AD-64298 A-128427 GfsusUfgGfaUfgUfGfUfcUfgCfgGfcGfuUfL96 593 A-128428 asAfscGfcCfgCfaGfacaCfaUfcCfaAfcsgsa 808
AD-64299 A-128441 UfsusCfaUfcCfiiGfCfUfgCfuAfuGfcCfiiAfL96 594 A-128442 usAfsgGfcAfuAfgCfagcAfgGfaUfgAfasgsa 809
AD-64300 A-128371 UfsusCfuUfgUfuGfAfCfaAfaAfaUfcCfuAfL96 595 A-128372 usAfsgGfaUfuUfuUfgucAfaCfaAfgAfasasa 810
AD-64302 A-128417 UfsasUfaUfgGfaUfGfAfuGfuGfgUfaUfuAfL96 596 A-128418 usAfsaUfaCfcAfcAfiicaUfcCfaUfaUfasasc 811
AD-64303 A-128429 UfsusCfaUfcCfuGfCfUfgCftiAfiiGfcCfiiCfL96 597 A-128430 gsAfsgGfcAfuAfgCfagcAfgGfaUfgAfasgsa 812
AD-64304 A-128443 GfsusGfcAfcUfuCfGfCfuUfcAfcCfuCfuAfL96 598 A-128444 usAfsgAfgGftiGfaAfgcgAfaGfijGfcAfcsasc 813
AD-64305 A-128373 UfsusGfaCfaAfaAfAfUfcCfuCfaCfaAfuAfL96 599 A-128374 usAfsuUfgUfgAfgGfauuUftiUfgUfcAfascsa 814
113
Duplex Naine Sense Oligo Namc Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-64307 A-128403 AfsasGfcCfuCfcAfAfGfcUfgUfgCfcUfuAfL96 600 A-128404 usAfsaGfgCfaCfaGfcuuGfgAfgGfcUfusgsa 815
AD-64308 A-128419 CfscsUfcUfuCfaUflCfCfiiGfcUfgCfuAfuAfL96 601 A-128420 usAfsuAfgCfaGfcAfggaUfgAfaGfaGfgsasa 816
AD-64309 A-128431 CfscsUfgCfuGfcUfAfUfgCfcUfcAfiiCfuUfL96 602 A-128432 asAfsgAfiiGfaGfgCfauaGfcAfgCfaGfgsasu 817
AD-64310 A-128375 CfsasUfcUfuCfuUfGfUfuGfgUfuCfuUfcUfL96 603 A-128376 asGfsaAfgAfaCfcAfacaAfgAfaGfaUfgsasg 818
AD-64311 A-128391 CfscsGfiiCfuGfuGfCfCfuUfcUfcAfuCfuAfL96 604 A-128392 usAfsgAfuGfaGfaAfggcAfcAfgAfcGfgsgsg 819
AD-64312 A-l 28405 CfscsUfcAfiiCfuUfCfUfuGfuUfgGfuUfcUfL96 605 A-128406 asGfsaAfcCfaAfcAfagaAfgAfuGfaGfgscsa 820
AD-64313 A-128421 CfscsAfcCfaAfaUfGfCfcCfcUfaUfcUftiAfL96 606 A-128422 usAfsaGfaUfaGfgGfgcaUfiiUfgGfuGfgsusc 821
AD-64314 A-128433 GfscsUfcCfuCfuGfCfCfgAfuCfcAfuAfcUfL96 607 A-128434 asGfsuAfuGfgAfuCfggcAfgAfgGfaGfcscsa 822
AD-64315 A-l 28363 GfsusUfgAfcAfaAfAfAfuCfcUfcAfcAfaUfL96 608 A-128445 PasUfsuGfuGfaGfgAfiiuuUfuGfiiCfaAfcsasa 823
AD-64316 A-128377 UfsgsUfiiGfaCfaAfAfAfaUfcCfuCfaCfaAfL96 609 A-128453 PusUfsgUfgAfgGfaUfiiuuUfgUfcAfaCfasasg 824
AD-64317 A-128393 GfsgsUfgGfaCfuUfCfUfcUfcAfaUfuUfuAfL96 610 A-128461 PusAfsaAfaUfiiGfaGfagaAfgUfcCfaCfcsasc 825
AD-64318 A-l 28407 UfscsUfuUfiiGfgAfGfUfgUfgGfaUfuCfgAfL96 611 A-l 28469 PusCfsgAfaUfcCfaCfacuCfcAfaAfaGfascsa 826
AD-64319 A-128423 AfscsUfgUfuCfaAfGfCfcUfcCfaAfgCfuAfL96 612 A-l 28477 PusAfsgCfuUfgGfaGfgcuUfgAfaCfaAfgsasc 827
AD-64320 A-128435 UfscsUfgCfcGfaUfCfCfaUfaCfuGfcGfgAfL96 613 A-128483 PusCfscGfcAfgUfaUfggaUfcGfgCfaGfasgsg 828
AD-64321 A-123463 AfsgsUfiiAfuAfiiGfGfAftiGfaUfgUfgGfiiAfL96 614 A-128446 PusAfscCfaCfaUfcAfiiccAfiiAfuAfaCfusgsa 829
AD-64322 A-128379 AfsusGfuGfuCfuGfCfGfgCfgUfuUfuAfiiAfL96 615 A-l 28454 PusAfsuAfaAfaCfgCfcgcAfgAfcAfcAfuscsc 830
AD-64323 A-128395 CfscsCfcGfuCfiiGfUfGfcCfuUfcUfcAfuAfL96 616 A-128462 PusAfsuGfaGfaAfgGfcacAfgAfcGfgGfgsasg 831
AD-64324 A-128409 GfscsCfuAfaUfcAfUfCfuCfiiUfgUfiiCfaUfL96 617 A-128470 PasUfsgAfaCfaAfgAfgauGfaUfuAfgCfgsasg 832
AD-64325 A-128425 UfscsUfaGfaCfuCfGfUfgGfiiGfgAfcUfuCfL96 618 A-128478 PgsAfsaGfuCfcAfcCfacgAfgUfcUfaGfascsu 833
AD-64326 A-128437 CfsusGfcCfgAfuCfCfAfiiAfcUfgCfgGfaAfL96 619 A-128484 PusUfscCfgCfaGftiAfuggAfuCfgGfcAfgsasg 834
AD-64328 A-128381 AfsusCfuUfcUfuGfUfUfgGfiiUfcUfiiCftiAfL96 620 A-128455 PusAfsgAfaGfaAfcCfaacAfaGfaAfgAfiisgsa 835
AD-64330 A-128411 UfsusCfuCfuCfaAfUfUftiUfcUfaGfgGfgAfL96 621 A-128471 PusCfscCfcUfaGfaAfaauUfgAfgAfgAfasgsu 836
AD-64331 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 622 A-127907 PusGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 837
AD-64332 A-128001 GfsusGfcAfcUfuCfGfCfuUfcAfcCfuCfaG 623 A-128485 PcsAfsgAfgGftiGfaAfgcgAfaGfuGfcAfcsasc 838
AD-64333 A-128367 GfsusUftiUfuCfuUfGfUfuGfaCfaAfaAfaUfL96 624 A-128448 PasUfsuUfuUfgUfcAfacaAfgAfaAfaAfcscsc 839
AD-64334 A-128383 CfsusGfcCfuAfaUfCfAfiiCfuCfuUfgUfuAfL96 625 A-128456 PusAfsaCfaAfgAfgAfugaUftiAfgGfcAfgsasg 840
114
19808 «
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-64335 A-128399 UfscsCfiiCfaCfaAfUfAfcCfaCfaGfaGfuAfL96 626 A-128464 PusAfscUfcUfgUfgGfuauUfgUfgAfgGfasusu 841
AD-64336 A-128413 CfsusUfgUfuGfaCfAfAfaAfaUfcCfuCfaAfL96 627 A-128472 PusUfsgAfgGfaUfuUfuugUfcAfaCfaAfgsasa 842
AD-64337 A-127955 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 628 A-127958 PasAfsaUfuGfaGfaGfaagUfcCfaCfcAfcsgsa 843
AD-64338 A-128439 GfscsAfaCfuUfuUfUfCfaCfcUfcUfgCfcUfL96 629 A-128486 PasGfsgCfaGfaGfgUfgaaAfaAfgUfuGfcsasu 844
AD-64339 A-128369 GfsgsGfaAfcAfaGfAfGfcUfaCfaGfcAfiiAfL96 630 A-128449 PusAfsuGfcUfgUfaGfcucUfuGfuUfcCfcsasa 845
AD-64341 A-128401 UfscsAfiiCfuUfcUfUfGfiiUfgGfiiUfcUfuAfL96 631 A-128465 PusAfsaGfaAfcCfaAfcaaGfaAfgAfuGfasgsg 846
AD-64342 A-128415 CfsusGfcUfgCftiAfUfGfcCfuCfaUfcUfiiAfL96 632 A-128473 PusAfsaGfaUfgAfgGfcauAfgCfaGfcAfgsgsa 847
AD-64343 A-128427 GfsusUfgGfaUfgUfGfUfcUfgCfgGfcGfuUfL96 633 A-128479 PasAfscGfcCfgCfaGfacaCfaUfcCfaAfcsgsa 848
AD-64344 A-128441 UfsusCfaUfcCfuGfCfUfgCfuAfuGfcCfuAfL96 634 A-128487 PusAfsgGfcAfuAfgCfagcAfgGfaUfgAfasgsa 849
AD-64345 A-128371 UfsusCfuUfgUfuGfAfCfaAfaAfaUfcCfuAfL96 635 A-128450 PusAfsgGfaUfuUfuUfgucAfaCfaAfgAfasasa 850
AD-64347 A-123487 GfsgsAfuGfiiGfiiCfUfGfcGfgCfgUfuUfiiAfL96 636 A-128466 PusAfsaAfaCfgCfcGfcagAfcAfcAfuCfcsasg 851
AD-64348 A-128417 UfsasUfaUfgGfaUiGfAfijGfuGfgUfaUfuAfL96 637 A-128474 PusAfsaUfaCfcAfcAfucaUfcCfaUfaUfasasc 852
AD-64349 A-128429 UfsusCfaUfcCfuGfCfUfgCfiiAfiiGfcCfuCfL96 638 A-128480 PgsAfsgGfcAftiAfgCfagcAfgGfaUfgAfasgsa 853
AD-64350 A-128443 GfsusGfcAfcUfuCfGfCfiiUfcAfcCfiiCfiiAfL96 639 A-128488 PusAfsgAfgGfuGfaAfgcgAfaGfiiGfcAfcsasc 854
AD-64351 A-128373 UfsusGfaCfaAfaAfAfUfcCftiCfaCfaAfuAfL96 640 A-l 28451 PusAfsuUfgUfgAfgGfauuUfiiUfgUfcAfascsa 855
AD-64352 A-128389 CfscsAfaGfuGfuUfUfGfcUfgAfcGfcAfaAfL96 641 A-128459 PusUfsuGfcGfuCfaGfcaaAfcAfcUfuGfgscsa 856
AD-64352 A-128389 CfscsAfaGfuGfuUfUfGfcUfgAfcGfcAfaAfL96 642 A-128459 PusUfsuGfcGfuCfaGfcaaAfcAfcUfiiGfgscsa 857
AD-64353 A-128403 AfsasGfcCfiiCfcAfAfGfcUfgUfgCfcUfuAfL96 643 A-128467 PusAfsaGfgCfaCfaGfcuuGfgAfgGfcUfusgsa 858
AD-64354 A-128419 CfscsUfcUfiiCfaUfCfCfuGfcUfgCfiiAfiiAfL96 644 A-128475 PusAfsuAfgCfaGfcAfggaUfgAfaGfaGfgsasa 859
AD-64355 A-128431 CfscsUfgCfuGfcUfAfUfgCfcUfcAfuΠ645 A-128481 PasAfsgAfuGfaGfgCfauaGfcAfgCfaGfgsasu 860
AD-64356 A-128375 CfsasUfcUfuCfuUfGfUfuGfgUfuCfuUfcUfL96 646 A-128452 PasGfsaAfgAfaCfcAfacaAfgAfaGfaUfgsasg 861
AD-64357 A-128391 CfscsGfuCfuGfuGfOfCfuUfcUfcAfuC 647 A-l 28460 PusAfsgAfuGfaGfaAfggcAfcAfgAfcGfgsgsg 862
AD-64358 A-128405 CfscsUfcAfuCfuUfCfUfuGfiiUfgGfuUfcUfL96 648 A-128468 PasGfsaAfcCfaAfcAfagaAfgAfuGfaGfgscsa 863
AD-64359 A-128421 CfscsAfcCfaAfaUfGfCfcCfcUfaUfcUfuAfL96 649 A-128476 PusAfsaGfaUfaGfgGfgcaUfiiUfgGfiiGfgsusc 864
AD-64360 A-128433 GfscsUfcCfuCfuGfCfCfgAfiiCfcAfuAfcUfL96 650 A-128482 PasGfsuAfiiGfgAfuCfggcAfgAfgGfaGfcscsa 865
AD-64700 A-129379 ascsucguggugdTacuu(Cgn)ucucaL96 651 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 866
115
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-64701 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 652 A-129387 PusgsagagaagdTccadCcacgaguscsii 867
AD-64702 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 653 A-129395 usGsagadGaaguccaCcacgaguscsu 868
AD-64703 A-129376 ascsucguggugdGacuucdAcucaL96 654 A-129385 usdGsagagaagdTccadCcacgaguscsu 869
AD-64704 A-129381 ascsucguggdTgdTacuucdAcucaL96 655 A-129389 usdGsagadGaaguccadCcacgaguscsu 870
AD-64705 A-129380 ascsucguggugdTacuucdAcucaL96 656 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 871
AD-64706 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 657 A-129388 usdGsadGagaaguccadCcacgaguscsu 872
AD-64707 A-127905 AfscsUfcGfuGfgUiGfGfaCfuUfcUfcUfcA 658 A-129396 usgsagadGaagdTccadCcacgaguscsu 873
AD-64708 A-129382 ascsucguggdTgdGacuuc(Tgn)cucaL96 659 A-129385 usdGsagagaagdTccadCcacgaguscsu 874
AD-64709 A-129373 ascsucguggugdGacuu(Cgn)ucucaL96 660 A-129391 usdGsagadGaagdTccadCcacgaguscsu 875
AD-64710 A-129373 ascsucguggugdGacuu(Cgn)ucucaL96 661 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 876
AD-64711 A-129381 ascsucguggdTgdTacuucdAcucaL96 662 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 877
AD-64712 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 663 A-129389 usdGsagadGaaguccadCcacgaguscsu 878
AD-64713 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 664 A-129397 PusgsagadGaagdTccadCcacgaguscsu 879
AD-64714 A-129384 ascsucguggdTgdGacuucdAcucaL96 665 A-129385 usdGsagagaagdTccadCcacgaguscsu 880
AD-64715 A-129376 ascsucguggugdGacuucdAcucaL96 666 A-129391 usdGsagadGaagdTccadCcacgaguscsu 881
AD-64716 A-129374 ascsucguggugdGacuucu(Cgn)ucaL96 667 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 882
AD-64717 A-129382 ascsucguggdTgdGacuuc(Tgn)cucaL96 668 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 883
AD-64718 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 669 A-129390 usdGsagagadAguccadCcacgaguscsu 884
AD-64719 A-127917 ascsucguggugdGacuuc(Tgn)cucaL96 670 A-129385 usdGsagagaagdTccadCcacgaguscsu 885
AD-64720 A-129381 ascsucguggdTgdTacuucdAcucaL96 671 A-129385 usdGsagagaagdTccadCcacgaguscsu 886
AD-64721 A-129382 ascsucguggdTgdGacuuc(Tgn)cucaL96 672 A-129391 usdGsagadGaagdT ccadCcacgaguscsu 887
AD-64722 A-129375 ascsucguggugdGacuucY34cucaL96 673 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 888
AD-64723 A-129383 ascsucguggugdGdAcuuc(Tgn)cucaL96 674 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 889
AD-64725 A-127917 ascsucguggugdGacuuc(Tgn)cucaL96 675 A-129398 PusdGsagagaagdTccadCcacgaguscsu 890
AD-64726 A-129373 ascsucguggugdGacuu(Cgn)ucucaL96 676 A-129389 usdGsagadGaaguccadCcacgaguscsu 891
AD-64727 A-129384 ascsucguggdTgdGacuucdAcucaL96 677 A-129391 usdGsagadGaagdTccadCcacgaguscsu 892
116
Duplex Name Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-64728 A-129376 ascsucguggugdGacuucdAcucaL96 678 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfiiscsu 893
AD-64729 A-129384 ascsucguggdTgdGacuucdAcucaL96 679 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 894
AD-64730 A-127905 AfscsUfcGfuGfgUfGfGfaCftiUfcUfcUfcAfL96 680 A-129392 usGsagagaagdTccadCcacgaguscsu 895
AD-64731 A-129399 Y34ascsucguggugdGacuuc(Tgn)cucaL96 681 A-129385 usdGsagagaagdTccadCcacgaguscsu 896
AD-64732 A-129376 ascsucguggugdGacuucdAcucaL96 682 A-129389 usdGsagadGaaguccadCcacgaguscsu 897
AD-64733 A-129381 ascsucguggdTgdTacuucdAcucaL96 683 A-129391 usdGsagadGaagdTccadCcacgaguscsu 898
AD-64734 A-129377 ascsucguggugdGacuucdCcucaL96 684 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 899
AD-64735 A-127905 AfscsUfcGfuGfgUfGfGfaCfiiUfcUfcUfcAfL96 685 A-129385 usdGsagagaagdT ccadCcacgaguscsu 900
AD-64736 A-127905 AfscsUfcGfuGfgUfGfGfaCftiUfcUfcUfcAfL96 686 A-129393 usdGsagagaagdTccaCcacgaguscsu 901
AD-64737 A-129399 Y34ascsucguggugdGacuuc(Tgn)cucaL96 687 A-129398 PusdGsagagaagdTccadCcacgaguscsu 902
AD-64738 A-129382 ascsucguggdTgdGacuuc(Tgn)cucaL96 688 A-129389 usdGsagadGaaguccadCcacgaguscsu 903
AD-64739 A-129378 ascsucguggugdGacuucdGcucaL96 689 A-127906 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 904
AD-64740 A-127905 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 690 A-129386 usgsagagaagdTccadCcacgaguscsu 905
AD-64741 A-127905 AfscsUfcGfiiGfgUfGfGfaCfuUfcUfcUfcAfL96 691 A-129394 usGsagagaagdTccaCcacgaguscsu 906
AD-64742 A-129373 ascsucguggugdGacuu(Cgn)ucucaL96 692 A-129385 usdGsagagaagdTccadCcacgaguscsu 907
AD-64743 A-129384 ascsucguggdTgdGacuucdAcucaL96 693 A-129389 usdGsagadGaaguccadCcacgaguscsu 908
Table 4. Unmodificd Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
Duplex ID Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-65369 UCGUGGUGGACUUCUCUCA 909 UGAGAGAAGUCCACCACGAUU 938
AD-65381 UCGUGGUGGACUUCUCUCA 910 UGAGAGAAGUCCACCACGAUU 939
AD-63962 UCGUGGUGGACUUCUCUCA 911 UGAGAGAAGUCCACCACGAUU 940
117
Duplex ID Sense Scqucncc (5’ to 3’) SEQ ID NO: Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-63938 ACUCGUGGUGGACUUCUCUCA 912 UGAGAGAAGUCCACCACGAGUCU 941
AD-65561 UCGUGGUGGACUUCUCUCA 913 UGAGAGAAGUCCACCACGAUU 942
AD-65566 UCGUGGUGGACUUCUCUCA 914 UGAGAGAAGUCCACCACGAUU 943
AD-63944 UCGUGGUGGACUUCUCUCAUU 915 UGAGAGAAGUCCACCACGAUU 944
AD-63968 ACUCGUGGUGGACUUCUCUCA 916 UGAGAGAAGUCCACCACGAGUCU 945
AD-65406 UCGUGGUGGACUUCUCUCA 917 UGAGAGAAGUCCACCACGAUU 946
AD-65396 ACUCGUGGUGGACUUCUCUCA 918 UGAGAGAAGUCCACCACGAGUUU 947
AD-65427 GUGCACUUCGCUUCACCUCUA 919 UAGAGGUGAAGCGAAGUGCACUU 948
AD-65573 GUGCACUUCGCUUCACCUCUA 920 UAGAGGUGAAGCGAAGUGCACAC 949
AD-65432 GCACUUCGCUUCACCUCUA 921 UAGAGGUGAAGCGAAGUGCAC 950
AD-64332 GUGCACUUCGCUUCACCUCUG 922 CAGAGGUGAAGCGAAGUGCACAC 951
AD-64322 AUGUGUCUGCGGCGUUUUAUA 923 UAUAAAACGCCGCAGACACAUCC 952
AD-64272 GUGCACUUCGCUUCACCUCUG 924 CAGAGGUGAAGCGAAGUGCACAC 953
AD-65583 GCACUUCGCUUCACCUCUA 925 UAGAGGUGAAGCGAAGUGCUU 954
AD-63994 GGUGGACUUCUCUCAAUUU 926 AAAUUGAGAGAAGUCCACCAC 955
AD-65370 CGUGGUGGACUUCUCUCAAUU 927 AAUUGAGAGAAGUCCACCAGCAG 956
AD-65265 GUGGUGGACUUCUCUCAAUUU 928 AAAUUGAGAGAAGUCCACCACGA 957
AD-65407 CGUGGUGGACUUCUCUCAAUU 929 AAUUGAGAGAAGUCCACCAGCAG 958
AD-64027 GGUGGACUUCUCUCAAUUU 930 AAAUUGAGAGAAGUCCACCAC 959
AD-65266 GUGGUGGACUUCUCUCAAUUU 931 AAAUUGAGAGAAGUCCACCACGA 960
AD-65389 UGGUGGUCTUCUCUAAAUU 932 AAUUGAGAGAAGUCCACCAUU 961
AD-64008 GUGGUGGACUUCUCUCAAUUU 933 AAAUUGAGAGAAGUCCACCACGA 962
AD-65377 CGUGGUGGUCTUCUCUAAAUU 934 AAUUGAGAGAAGUCCACCAGCUU 963
AD-65409 GGUGGACUUCUCUCAAUUUUA 935 UAAAAUUGAGAGAAGUCCACCAC 964
AD-65403 GGUGGACUUCUCUCAAUUUUA 936 UAAAAUUGAGAGAAGUCCACCAC 965
AD-65385 UGGACUACTCUCAAAUUUA 937 UAAAAUUGAGAGAAGUCCAUU 966
118
Table 5. Exemplary Modified Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
DuplexID Sense Sequence (5' to 3') SEQ ID NO: Antisense Sequence (5' to 3') SEQ ID NO:
AD-65369 uscsguGfgUfGfGfacuuCfUfcucaL96 967 PusGfsagaGfaAfGfuccaCfcAfcgasusu 996
AD-65381 uscsguGfgUfGfGfacuucucucaL96 968 PusGfsagaGfaAfGfuccaCfcAfcgasusu 997
AD-63962 Y44uscsGfuGfgUfgGfaCfuUfcUfcUfcAfY44 969 PusGfsaGfaGfaAfgUfcCfaCfcAfcGfasusu 998
AD-63938 Y44ACUCGUGGUGGACUUCUCUCA 970 UGAGAGAAGUCCACCACGAGUCU 999
AD-65561 uscsguGfgUfGfGfacuuCfUfcucaL96 971 UfsGfsagaGfaAfGfuccaCfcAfcgasusu 1000
AD-65566 uscsguGfgUfGfGfacuucucucaL96 972 UfsGfsagaGfaAfGfuccaCfcAfcgasusu 1001
AD-63944 Y44ucGuGGuGGAcuucucucAusuY44 973 UfGfagAfgAfAfGUfccaCfCAfcgAusu 1002
AD-63968 AfscsUfcGfuGfgUfGfGfaCfuUfcUfcUfcAfL96 974 usGfsaGfaGfaAfgUfccaCfcAfcGfaGfuscsu 1003
AD-65406 uscsguGfgUfGfGfacuuCfUfcucaL96 975 usGfsagaGfaAfGfuccaCfcAfcgasusu 1004
AD-65396 ascsucguGfgUfGfGfacuucucucaL96 976 usGfsagaGfaaguccaCfcAfcgagususu 1005
AD-65427 gsusgcacUfiiCfGfCfiiucaccucuaL96 977 PusAfsgagGfugaagcgAfaGfugcacsusu 1006
AD-65573 gsusgcacUfuCfGfCfuucaCfCfucuaL96 978 UfsAfsgagGfuGfAfagcgAfaGfugcacsasc 1007
AD-65432 gscsacUfucGfCfuucacCfucuaL96 979 PusAfsgagGfuGfAfagcgAfaGfugcsasc 1008
AD-64332 GfsusGfcAfcUfuCfGfCfuUfcAfcCfuCfuGfL96 980 PcsAfsgAfgGfuGfaAfgcgAfaGfiiGfcAfcsasc 1009
AD-64322 AfsusGfuGfuCfuGfCfGfgCfgUfiiUfuAfuAfL96 981 PusAfsuAfaAfaCfgCfcgcAfgAfcAfcAfuscsc 1010
AD-64272 GfsusGfcAfcUfuCfGfCfuUfcAfcCfuCfuGfL96 982 csAfsgAfgGfuGfaAfgcgAfaGfuGfcAfcsasc 1011
AD-65583 gscsacuucgdCuucac(Cgn)ucuaL96 983 usdAsgagdGugaagcgdAagugcsusu 1012
AD-63994 gsgsUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 984 PasAfsaUfuGfaGfaGfaagUfcCfaCfcsasc 1013
AD-65370 csgsugguGfgAfCfUfucucUfCfaauuL96 985 asAfsuugAfgAfGfaaguCfcAfccagcsasg 1014
AD-65265 gsusggugGfaCfUfUfcUfcucaauuuL96 986 asAfsaUfugagaGfaagUfcCfaccAfcsgsa 1015
AD-65407 csgsugguGfgAfCfUfucucUfCfaauuL96 987 asAfsuugAfgAfgAfaguCfcAfccagcsasg 1016
AD-64027 gsgsUfgGfaCfUfUfcUfcUfcAfaUfiiUfL96 988 asAfsaUfuGfaGfaGfaagUfcCfaCfcsasc 1017
AD-65266 gsusggugGfaCfUfUfcucuCfaauuuL96 989 asAfsaUfiigagaGfaagUfcCfaccAfcsgsa 1018
119
DuplcxID Sense Sequence (5’ to 3') SEQ ID NO: Antisense Sequence (5' to 3') SEQ ID NO:
AD-65389 usgsgudGgucdTucucuaaauuL96 990 asdAsuugagagdAagudCcaccasusu 1019
AD-64008 GfsusGfgUfgGfaCfUfUfcUfcUfcAfaUfuUfL96 991 asAfsaUfiiGfaGfaGfaagUfcCfaCfcAfcsgsa 1020
AD-65377 csgsuggudGgucdTucucuaaauuL96 992 asdAsuugagagdAagudCcaccagcsusu 1021
AD-65409 gsgsuggaCfuUfCfUfcucaAfUfiiuuaL96 993 PusAfsaaaUfuGfAfgagaAfgUfccaccsasc 1022
AD-65403 gsgsuggaCfuUfUfUfcucaAfUfuuuaL96 994 usAfsaaaUfuGfAfgagaAfgUfccaccsasc 1023
AD-65385 usgsgacuacdTcucaaauuuaL96 995 usdAsaaauugadGagadAguccasusu 1024
Table 6. Exemplary Unmodified Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
Duplex ID Sense ID Sense Sequence Unmodified (5' to 3') SEQ ID NO: Antisense ID Antisense Sequence Unmodified (5’ to 3’) SEQ ID NO:
AD-65381 A-130366 UCGUGGUGGACUUCUCUCA 1025 A-l 31904 UGAGAGAAGUCCACCACGAUU 1036
AD-66019 A-130366 UCGUGGUGGACUUCUCUCA 1026 A-131904 UGAGAGAAGUCCACCACGAUU 1037
AD-65375 A-130366 UCGUGGUGGACUUCUCUCA 1027 A-130364 UGAGAGAAGUCCACCACGAUU 1038
AD-65427 A-130441 GUGCACUUCGCUUCACCUCUA 1028 A-131905 UAGAGGUGAAGCGAAGUGCACUU 1039
AD-66110 A-130441 GUGCACUUCGCUUCACCUCUA 1029 A-131905 UAGAGGUGAAGCGAAGUGCACUU 1040
AD-65421 A-130441 GUGCACUUCGCUUCACCUCUA 1030 A-130442 UAGAGGUGAAGCGAAGUGCACUU 1041
AD-65407 A-130371 CGUGGUGGACUUCUCUCAAUU 1031 A-130372 AAUUGAGAGAAGUCCACCAGCAG 1042
AD-65377 A-l 30384 CGUGGUGGUCTUCUCUAAAUU 1032 A-130748 AAUUGAGAGAAGUCCACCAGCUU 1043
Duplex ID Sense ID Sense Sequence Unmodifïed (5* to 3') SEQ ID NO: Antisense ID Antisense Sequence Unmodifïed (5’ to 3’1 SEQID NO:
AD-65409 A-130388 GGUGGACUUCUCUCAAUUUUA 1033 A-131906 UAAAAUUGAGAGAAGUCCACCAC 1044
AD-66111 A-130388 GGUGGACUUCUCUCAAUUUUA 1034 A-131906 UAAAAUUGAGAGAAGUCCACCAC 1045
AD-65403 A-130388 GGUGGACUUCUCUCAAUUUUA 1035 A-130389 UAAAAUUGAGAGAAGUCCACCAC 1046
Table 7. Exemplary Modified Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
Duplex ID Sense ID Sense Sequence (5' to 3') SEQ ID NO: Antisense ID Antisense Sequence (5' to 3') SEQ ID NO:
AD-65381 A-130366 uscsguGfgUfGfGfacuucucucaL96 1047 A-131904 PusGfsagaGfaAfGfuccaCfcAfcgasusu 1058
AD-66019 A-130366 uscsguGfgUfGfGfacuucucucaL96 1048 A-131904 VPusGfsagaGfaAfGfuccaCfcAfcgasusu 1059
AD-65375 A-130366 uscsguGfgUfGfGfacuucucucaL96 1049 A-130364 usGfsagaGfaAfGfiiccaCfcAfcgasusu 1060
AD-65427 A-130441 gsusgcacUfuCfGfCfuucaccucuaL96 1050 A-131905 PusAfsgagGfugaagcgAfaGfugcacsusu 1061
AD-66110 A-130441 gsusgcacUftiCfGfCfuucaccucuaL96 1051 A-l 31905 VPusAfsgagGfugaagcgAfaGfugcacsusu 1062
AD-65421 A-130441 gsusgcacUfuCfGfCftiucaccucuaL96 1052 A-130442 usAfsgagGfugaagcgAfaGftigcacsusu 1063
AD-65407 A-130371 csgsugguGfgAfCfUfiicucUfCfaauuL96 1053 A-l 30372 asAfsuugAfgAfgAfaguCfcAfccagcsasg 1064
AD-65377 A-l 30384 csgsuggudGgucdTucucuaaauuL96 1054 A-l 30748 asdAsuugagagdAagudCcaccagcsusu 1065
121 β
Duplex ID Sense ID Sense Sequence (5' to 3') SEQ ID NO: Antisense ID Antisense Sequence (5' to 3') SEQ ID NO:
AD-65409 A-130388 gsgsuggaCfuUfCfUfcucaAfUfuuuaL96 1055 A-131906 PusAfsaaaUfuGfAfgagaAfgUfccaccsasc 1066
AD-66111 A-130388 gsgsuggaCfuUfCfUfcucaAfUfiiuuaL96 1056 A-131906 VPusAfsaaaUfiiGfAfgagaAfgUfccaccsasc 1067
AD-65403 A-130388 gsgsuggaCfuUfCfUfcucaAfUfuuuaL96 1057 A-l 30389 usAfsaaaUfuGfAfgagaAfgUfccaccsasc 1068
Table 8. Exemplary Unmodified Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
DuplexID Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense OligoName Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-65776 A-131859 UGUGCACUUCGCUUCACCUCU 1069 A-l 31860 AGAGGUGAAGCGAAGUGCACACG 1115
AD-65782 A-131877 UGCACUUCGCUUCACCUCUGA 1070 A-l 31878 UCAGAGGUGAAGCGAAGUGCACA 1116
AD-65792 A-131865 GUGUGCACUUCGCUUCACCUA 1071 A-l 31866 UAGGUGAAGCGAAGUGCACACGG 1117
AD-65781 A-131861 CGUGUGCACUUCGCUUCACCU 1072 A-l 31862 AGGUGAAGCGAAGUGCACACGGU 1118
AD-64304 A-128443 GUGCACUUCGCUUCACCUCUA 1073 A-128444 UAGAGGUGAAGCGAAGUGCACAC 1119
AD-65771 A-131857 CCGUGUGCACUUCGCUUCACA 1074 A-131858 UGUGAAGCGAAGUGCACACGGUC 1120
AD-65758 A-l 31867 CACUUCGCUUCACCUCUGCAA 1075 A-l 31868 UUGCAGAGGUGAAGCGAAGUGCA 1121
AD-65777 A-131875 ACUUCGCUUCACCUCUGCACA 1076 A-131876 UGUGCAGAGGUGAAGCGAAGUGC 1122
AD-61567 A-123525 GGCUGUAGGCAUAAAUUGGUA 1077 A-123526 UACCAAUUUAUGCCUACAGCCUC 1123
AD-65772 A-131873 UUCGCUUCACCUCUGCACGUA 1078 A-l 31874 UACGUGCAGAGGUGAAGCGAAGU 1124
AD-65767 A-131871 UCGCUUCACCUCUGCACGUCA 1079 A-131872 UGACGUGCAGAGGUGAAGCGAAG 1125
AD-65763 A-131869 CUUCGCUUCACCUCUGCACGU 1080 A-131870 ACGUGCAGAGGUGAAGCGAAGUG 1126
AD-64281 A-128395 CCCCGUCUGUGCCUUCUCAUA 1081 A-l 28396 UAUGAGAAGGCACAGACGGGGAG 1127
AD-64311 A-128391 CCGUCUGUGCCUUCUCAUCUA 1082 A-128392 UAGAUGAGAAGGCACAGACGGGG 1128
122
DuplexID Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense OligoName Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-65790 A-131837 CCAGCACCAUGCAACUUUUUA 1083 A-131838 UAAAAAGUUGCAUGGUGCUGGUG 1129
AD-65761 A-131841 CACCAGCACCAUGCAACUUUU 1084 A-131842 AAAAGUUGCAUGGUGCUGGUGCG 1130
AD-65786 A-131849 CACCAUGCAACUUUUUCACCU 1085 A-131850 AGGUGAAAAAGUUGCAUGGUGCU 1131
AD-65785 A-131835 CAAUGUCAACGACCGACCUUA 1086 A-131836 UAAGGUCGGUCGUUGACAUUGCA 1132
AD-65787 A-131863 CGCUUCACCUCUGCACGUCGA 1087 A-131864 UCGACGUGCAGAGGUGAAGCGAA 1133
AD-65770 A-131845 ACCUUGAGGCAUACUUCAAAG 1088 A-131846 CUUUGAAGUAUGCCUCAAGGUCG 1134
AD-65766 A-131843 CCGACCUUGAGGCAUACUUCA 1089 A-131844 UGAAGUAUGCCUCAAGGUCGGUC 1135
AD-61555 A-123521 GACCUUGAGGCAUACUUCAAA 1090 A-l 23522 UUUGAAGUAUGCCUCAAGGUCGG 1136
AD-65762 A-131855 ACCGACCUUGAGGCAUACUUA 1091 A-131856 UAAGUAUGCCUCAAGGUCGGUCG 1137
AD-65755 A-l 31827 UCGCAUGGAGACCACCGUGAA 1092 A-l 31828 UUCACGGUGGUCUCCAUGCGACG 1138
AD-65788 A-131811 UUACAUAAGAGGACUCUUGGA 1093 A-131812 UCCAAGAGUCCUCUUAUGUAAGA 1139
AD-65768 A-131803 UCUUACAUAAGAGGACUCUUA 1094 A-131804 UAAGAGUCCUCUUAUGUAAGACC 1140
AD-61561 A-123523 ACUUCAAAGACUGUUUGUUUA 1095 A-123524 UAAACAAACAGUCUUUGAAGUAU 1141
AD-65764 A-131801 UACUUCAAAGACUGUUUGUUU 1096 A-l 31802 AAACAAACAGUCUUUGAAGUAUG 1142
AD-65753 A-131799 AUACUUCAAAGACUGUUUGUU 1097 A-l 31800 AACAAACAGUCUUUGAAGUAUGC 1143
AD-65765 A-131817 UUGUUUAAAGACUGGGAGGAA 1098 A-131818 UUCCUCCCAGUCUUUAAACAAAC 1144
AD-65769 A-131819 GCAUACUUCAAAGACUGUUUA 1099 A-131820 UAAACAGUCUUUGAAGUAUGCCU 1145
AD-65759 A-131815 CAAAGACUGUUUGUUUAAAGA 1100 A-131816 UCUUUAAACAAACAGUCUUUGAA 1146
AD-65774 A-131831 AGACUGUUUGUUUAAAGACUA 1101 A-l 31832 UAGUCUUUAAACAAACAGUCUUU 1147
AD-65778 A-131807 GUUUGUUUAAAGACUGGGAGA 1102 A-131808 UCUCCCAGUCUUUAAACAAACAG 1148
AD-65773 A-131805 GGGGGAGGAGAUUAGAUUAAA 1103 A-l 31806 UUUAAUCUAAUCUCCUCCCCCAA 1149
AD-65789 A-131825 GGGGAGGAGAUUAGAUUAAAG 1104 A-l 31826 CUUUAAUCUAAUCUCCUCCCCCA 1150
AD-65783 A-131809 GUUGGGGGAGGAGAUUAGAUU 1105 A-131810 AAUCUAAUCUCCUCCCCCAACUC 1151
AD-65754 A-131813 UUGGGGGAGGAGAUUAGAUUA 1106 A-131814 UAAUCUAAUCUCCUCCCCCAACU 1152
AD-65779 A-131821 GGGAGGAGAUUAGAUUAAAGA 1107 A-131822 UCUUUAAUCUAAUCUCCUCCCCC 1153
AD-65791 A-131851 UUAGAUUAAAGGUCUUUGUAA 1108 A-l 31852 UUACAAAGACCUUUAAUCUAAUC 1154
123
DupIexID Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense OligoName Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-65760 A-131829 UAGAUUAAAGGUCUUUGUACU 1109 A-131830 AGUACAAAGACCUUUAAUCUAAU 1155
AD-65784 A-131823 AUUAGAUUAAAGGUCUUUGUA 1110 A-131824 UACAAAGACCUUUAAUCUAAUCU 1156
AD-65757 A-131853 GAGGAGAUUAGAUUAAAGGUA 1111 A-131854 UACCUUUAAUCUAAUCUCCUCCC 1157
AD-65775 A-131847 GGACUCUUGGACUCUCUGCAA 1112 A-l 31848 UUGCAGAGAGUCCAAGAGUCCUC 1158
AD-65780 A-131833 ACUCUUGGACUCUCUGCAAUA 1113 A-l 31834 UAUUGCAGAGAGUCCAAGAGUCC 1159
AD-65756 A-l 31839 AGAUUAAAGGUCUUUGUACUA 1114 A-l 31840 UAGUACAAAGACCUUUAAUCUAA 1160
Table 9. Exemplary Unmodified Sense and Antisense Strand Sequences of HBV dsRNAs (Activity data available in WO2016/077321, incorporated herein by reference)
Duplex ID Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQID NO:
AD-65776 A-l31859 UfsgsUfgCfaCfuUfCfGfcUfuCfaCfcUfcUfL96 1161 A-131860 asGfsaGfgUfgAfaGfcgaAfgUfgCfaCfascsg 1207
AD-65782 A-l31877 UfsgsCfaCfuUfcGfCfUfuCfaCfcUfcUfgAfL96 1162 A-131878 usCfsaGfaGfgUfgAfagcGfaAfgUfgCfascsa 1208
AD-65792 A-l31865 GfsusGfuGfcAfcUfUfCfgCfiiUfcAfcCfuAfL96 1163 A-131866 usAfsgGfuGfaAfgCfgaaGfiiGfcAfcAfcsgsg 1209
AD-65781 A-131861 CfsgsUfgUfgCfaCfUfUfcGfcUfuCfaCfcUfL96 1164 A-l31862 asGfsgUfgAfaGfcGfaagUfgCfaCfaCfgsgsu 1210
AD-64304 A-128443 GfsusGfcAfcUfuCfGfCfuUfcAfcCfuCfuAfL96 1165 A-128444 usAfsgAfgGfuGfaAfgcgAfaGftiGfcAfcsasc 1211
AD-65771 A-131857 CfscsGfuGfuGfcAfCfUfuCfgCfuUfcAfcAfL96 1166 A-131858 usGfsuGfaAfgCfgAfaguGfcAfcAfcGfgsusc 1212
AD-65758 A-131867 CfsasCfuUfcGfcUfUfCfaCfcUfcUfgCfaAfL96 1167 A-131868 usUfsgCfaGfaGfgUfgaaGfcGfaAfgUfgscsa 1213
AD-65777 A-l31875 AfscsUfiiCfgCfuUfCfAfcCfuCfuGfcAfcAfL96 1168 A-131876 usGfsuGfcAfgAfgGfugaAfgCfgAfaGfiisgsc 1214
AD-61567 A-123525 GfsgsCfuGfuAfgGfCfAfuAfaAfuUfgGfuAfL96 1169 A-123526 usAfscCfaAfuUfuAfugcCfuAfcAfgCfcsusc 1215
AD-65772 A-131873 UfsusCfgCfuUfcAfCfCfuCfuGfcAfcGfiiAfL96 1170 A-l31874 usAfscGfuGfcAfgAfgguGfaAfgCfgAfasgsu 1216
AD-65767 A-131871 UfscsGfcUfuCfaCfCfUfcUfgCfaCfgUfcAfL96 1171 A-l31872 usGfsaCfgUfgCfaGfaggUfgAfaGfcGfasasg 1217
AD-65763 A-131869 CfsusUfcGfcUfuCfAfCfcUfcUfgCfaCfgUfL96 1172 A-131870 asCfsgUfgCfaGfaGfgugAfaGfcGfaAfgsusg 1218
AD-64281 A-128395 CfscsCfcGfiiCfuGfUfGfcCfuUfcUfcAfiiAfL96 1173 A-128396 usAfsuGfaGfaAfgGfcacAfgAfcGfgGfgsasg 1219
124
Duplex ID Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-64311 A-128391 CfscsGfuCfuGfuGfCfCfuUfcUfcAfuCfuAfL96 1174 A-128392 usAfsgAfuGfaGfaAfggcAfcAfgAfcGfgsgsg 1220
AD-65790 A-131837 CfscsAfgCfaCfcAfUfGfcAfaCfuUfuUfuAfL96 1175 A-l31838 usAfsaAfaAfgUfuGfcauGfgUfgCfuGfgsusg 1221
AD-65761 A-l31841 CfsasCfcAfgCfaCfCfAfuGfcAfaCfuUfuUfL96 1176 A-l31842 asAfsaAfgUfuGfcAfuggUfgCfuGfgUfgscsg 1222
AD-65786 A-l31849 CfsasCfcAfuGfcAfAfCfuUfuUfuCfaCfcUfL96 1177 A-131850 asGfsgUfgAfaAfaAfguuGfcAfuGfgUfgscsu 1223
AD-65785 A-l31835 CfsasAfuGfuCfaAfCfGfaCfcGfaCfcUfuAfL96 1178 A-131836 usAfsaGfgUfcGfgUfcguUfgAfcAfuUfgscsa 1224
AD-65787 A-131863 CfsgsCfuUfcAfcCfUfCfuGfcAfcGfuCfgAfL96 1179 A-131864 usCfsgAfcGfuGfcAfgagGfuGfaAfgCfgsasa 1225
AD-65770 A-l31845 AfscsCfuUfgAfgGfCfAfuAfcUfiiCfaAfaGfL96 1180 A-131846 csUfsuUfgAfaGfuAfugcCfuCfaAfgGfuscsg 1226
AD-65766 A-l31843 CfscsGfaCfcUfuGfAfGfgCfaUfaCfuUfcAfL96 1181 A-l31844 usGfsaAfgUfaUfgCfcucAfaGfgUfcGfgsusc 1227
AD-61555 A-123521 GfsasCfcUfuGfaGfGfCfaUfaCfuUfcAfaAfL96 1182 A-123522 usUfsuGfaAfgUfaUfgccUfcAfaGfgUfcsgsg 1228
AD-65762 A-l31855 AfscsCfgAfcCfuUfGfAfgGfcAfuAfcUfuAfL96 1183 A-131856 usAfsaGfuAfiiGfcCfiicaAfgGfuCfgGfuscsg 1229
AD-65755 A-131827 UfscsGfcAfuGfgAfGfAfcCfaCfcGfuGfaAfL96 1184 A-131828 usUfscAfcGfgUfgGfucuCfcAfiiGfcGfascsg 1230
AD-65788 A-131811 UfsusAfcAfuAfaGfAfGfgAfcUfcUfuGfgAfL96 1185 A-131812 usCfscAfaGfaGfuCfcucUfuAfiiGfuAfasgsa 1231
AD-65768 A-l31803 UfscsUfuAfcAfuAfAfGfaGfgAfcUfcUfuAfL96 1186 A-131804 usAfsaGfaGfuCfcUfcuuAfuGfuAfaGfascsc 1232
AD-61561 A-123523 AfscsUfiiCfaAfaGfAfCfuGfuUfuGfuUfiiAfL96 1187 A-123524 usAfsaAfcAfaAfcAfgucUfiiUfgAfaGfiisasu 1233
AD-65764 A-131801 UfsasCfuUfcAfaAfGfAfcUfgUfuUfgUfuUfL96 1188 A-131802 asAfsaCfaAfaCfaGfucuUfiiGfaAfgUfasusg 1234
AD-65753 A-l31799 AfsusAfcUfuCfaAfAfGfaCfuGfuUfuGfuUfL96 1189 A-131800 asAfscAfaAfcAfgUfcuuUfgAfaGfuAfiisgsc 1235
AD-65765 A-131817 UfsusGfuUfuAfaAfGfAfcUfgGfgAfgGfaAfL96 1190 A-131818 usUfscCfiiCfcCfaGfiicuUfuAfaAfcAfasasc 1236
AD-65769 A-131819 GfscsAfuAfcUfuCfAfAfaGfaCfuGfuUfuAfL96 1191 A-l31820 usAfsaAfcAfgUfcUfuugAfaGfuAfuGfcscsu 1237
AD-65759 A-131815 CfsasAfaGfaCfuGfUfUfuGfuUfuAfaAfgAfL96 1192 A-131816 usCfsuUfuAfaAfcAfaacAfgUfcUfuUfgsasa 1238
AD-65774 A-131831 AfsgsAfcUfgUfuUfGfUfuUfaAfaGfaCfuAfL96 1193 A-131832 usAfsgUfcUfuUfaAfacaAfaCfaGfuCfususu 1239
AD-65778 A-l31807 GfsusUfiiGfuUfuAfAfAfgAfcUfgGfgAfgAfL96 1194 A-131808 usCfsuCfcCfaGfuCfuuuAfaAfcAfaAfcsasg 1240
AD-65773 A-l31805 GfsgsGfgGfaGfgAfGfAfuUfaGfaUfuAfaAfL96 1195 A-131806 usUfsuAfaUfcUfaAfucuCfcUfcCfcCfcsasa 1241
AD-65789 A-l31825 GfsgsGfgAfgGfaGfAfUfuAfgAfuUfaAfaGfL96 1196 A-l31826 csUfsuUfaAfuCfuAfaucUfcCfuCfcCfcscsa 1242
AD-65783 A-l31809 GfsusUfgGfgGfgAfGfüfaGfaUfuAfgAfuUfL96 1197 A-131810 asAfsuCfuAfaUfcUfccuCfcCfcCfaAfcsusc 1243
AD-65754 A-131813 UfsusGfgGfgGfaGfGfAfgAfuUfaGfaUfuAfL96 1198 A-131814 usAfsaUfcUfaAfiiCfuccUfcCfcCfcAfascsu 1244
AD-65779 A-131821 GfsgsGfaGfgAfgAfUfUfaGfaUfuAfaAfgAfL96 1199 A-131822 usCfsuUfuAfaUfcUfaauCfuCfcUfcCfcscsc 1245
125
Duplex ID Sense Oligo Name Sense Sequence (5’ to 3’) SEQ ID NO: Antisense Oligo Name Antisense Sequence (5’ to 3’) SEQ ID NO:
AD-65791 A-131851 UfsusAfgAfuUfaAfAfGfgUfcUfuUfgUfaAfL96 1200 A-l31852 usUfsaCfaAfaGfaCfcuuUfaAfuCfuAfasusc 1246
AD-65760 A-l31829 UfsasGfaUfuAfaAfGfGfuCfuUfuGfuAfcUfL96 1201 A-131830 asGfsuAfcAfaAfgAfccuUfuAfaUfcUfasasu 1247
AD-65784 A-l31823 AfsusUfaGfaUfuAfAfAfgGfuCfuUftiGfuAfL96 1202 A-131824 usAfscAfaAfgAfcCfuuuAfaUfcUfaAfiiscsu 1248
AD-65757 A-l31853 GfsasGfgAfgAfiiUfAfGfaUfuAfaAfgGfuAfL96 1203 A-131854 usAfscCfiiUfuAfaUfcuaAfuCfuCfcUfcscsc 1249
AD-65775 A-l31847 GfsgsAfcUfcUfuGfGfAfcUfcUfcUfgCfaAfL96 1204 A-131848 usUfsgCfaGfaGfaGfuccAfaGfaGfiiCfcsusc 1250
AD-65780 A-131833 AfscsUfcUfuGfgAfCfUfcUfcUfgCfaAfuAfL96 1205 A-131834 usAfsuUfgCfaGfaGfaguCfcAfaGfaGfiiscsc 1251
AD-65756 A-l 31839 AfsgsAfuUfaAfaGfGfUfcUfuUfgUfaCfuAfL96 1206 A-l31840 usAfsgUfaCfaAfaGfaccUfuUfaAfuCfusasa 1252
Table 10. Exemplary Unmodified HBV X ORF Sense and Antisense Sequences. (Activity data available in WO2016/077321, incorporated herein by reference)
DupIcxID Sense Sequence Unmodified (5’ to 3’) SEQ ID NO: Antisense Sequence Umodified (5’ to 3’) SEQ IDNO:
AD-66808 GUCUGUGCCUUCUCAUCUA 1253 UAGAUGAGAAGGCACAGACUU 1263
AD-66809 GUCUGUGCCUUCUCAUCUA 1254 UAGAUGAGAAGGCACAGACUU 1264
AD-66810 GUGUGCACUUCGCUUCACA 1255 UGUGAAGCGAAGUGCACACUU 1265
AD-66811 GUGUGCACUUCGCUUCACA 1256 UGUGAAGCGAAGUGCACACUU 1266
AD-66812 UGUGCACUUCGCUUCACCUCU 1257 AGAGGUGAAGCGAAGUGCACAUU 1267
AD-66813 UGUGCACUUCGCUUCACCUCU 1258 AGAGGUGAAGCGAAGUGCACAUU 1268
AD-66814 CACCAGCACCAUGCAACUUUU 1259 AAAAGUUGCAUGGUGCUGGUGUU 1269
AD-66815 CACCAGCACCAUGCAACUUUU 1260 AAAAGUUGCAUGGUGCUGGUGUU 1270
AD-66816 CACCAUGCAACUUUUUCACCU 1261 AGGUGAAAAAGUUGCAUGGUGUU 1271
AD-66817 CACCAUGCAACUUUUUCACCU 1262 AGGUGAAAAAGUUGCAUGGUGUU 1272
126
Table 11. Exemplary Modified HBV X ORF Sense and Antisense Sequences. (Activity data available in WO2016/077321, incorporated herein by reference)
DuplexID Sense Sequence Modified (5’ to 3’) SEQ ID NO: Antisense Sequence Modified (5’ to 3’) SEQID NO:
AD-66808 gsuscuGfuGfCfCfuucucaucuaL96 1273 usAfsgauGfaGfAfaggcAfcAfgacsusu 1283
AD-66809 gsuscuGfuGfCfCfuucucaucuaL96 1274 UfsAfsgauGfaGfAfaggcAfcAfgacsusu 1284
AD-66810 gsusguGfcAfCfUfucgcuucacaL96 1275 usGfsugaAfgCfGfaaguGfcAfcacsusu 1285
AD-66811 gsusguGfcAfCfUfucgcuucacaL96 1276 UfsGfsugaAfgCfGfaaguGfcAfcacsusu 1286
AD-66812 usgsugcaCfùUfCfGfcuucaccucuL96 1277 asGfsaggUfgAfAfgcgaAfgUfgcacasusu 1287
AD-66813 usgsugcaCfuUfCfGfcuucaccucuL96 1278 AfsGfsaggUfgAfAfgcgaAfgUfgcacasusu 1288
AD-66814 csasccagCfaCfCfAfugcaacuuuuL96 1279 asAfsaagUfuGfCfauggUfgCfuggugsusu 1289
AD-66815 csasccagCfaCfCfAfiigcaacuuuuL96 1280 AfsAfsaagUfuGfCfauggUfgCfiiggugsusu 1290
AD-66816 csasccauGfcAfAfCfuuuuucaccuL96 1281 asGfsgugAfaAfAfaguuGfcAfuggugsusu 1291
AD-66817 csasccauGfcAfAfCfuuuuucaccuL96 1282 AfsGfsgugAfaAfAfaguuGfcAfuggugsusu 1292
127
Table 12: HBV Target Sequences, noting target sites on Accession No. X02763.1. (Activity data and exemplary Chemical modifications available at WO2012/024170, incorporated herein by reference)
Target Sequence Target Site SEQ Π) NO:
UCGUGGUGGACUUCUCÜCA 1663 1293
GUGGUGGACUUCUCUCAAU 1665 1294
GCCGAUCCAUACUGCGGAA 2669 1295
CCGAUCCAUACUGCGGAAC 2670 1296
CAUCCUGCUGCUAUGCCUC 1818 1297
UGCUGCUAUGCCUCAUCUU 1823 1298
GGUGGACUUCUCUCAAUUU 1667 1299
UGGUGGACUUCUCUCAAUU 1666 1300
UAGACUCGUGGUGGACUUC 1658 1301
UCCUCUGCCGAUCCAUACU 2663 1302
UGCCGAUCCAUACUGCGGA 2668 1303
UGGAUGUGUCUGCGGCGUU 1783 1304
CGAUCCAUACUGCGGAACU 2671 1305
CGCACCUCUCUUUACGCGG 2934 1306
CUGCCGAUCCAUACUGCGG 2667 1307
CGUGGUGGACUUCUCUCAA 1664 1308
CUGCUGCUAUGCCUCAUCU 1822 1309
CCUGCUGCUAUGCCUCAUC 1821 1310
CUAGACUCGUGGUGGACUU 1657 1311
UCCUGCUGCUAUGCCUCAU 1820 1312
GACUCGUGGUGGACUUCUC 1660 1313
AUCCAUACUGCGGAACUCC 2673 1314
CUCUGCCGAUCCAUACUGC 2665 1315
GAUCCAUACUGCGGAACUC 2672 1316
128
Target Sequence Target Sit< SEQ ID NO:
GAAGAACUCCCUCGCCUCG 567 1317
AAGCCUCCAAGCUGUGCCU 54 1318
AGAAGAACUCCCUCGCCUC 566 1319
GGAGUGUGGAUUCGCACUC 455 1320
CCUCUGCCGAUCCAUACUG 2664 1321
CAAGCCUCCAAGCUGUGCC 53 1322
UCCAUACUGCGGAACUCCU 2674 1323
CAGAGUCUAGACUCGUGGU 1651 1324
AAGAAGAACUCCCUCGCCU 565 1325
GAGUGUGGAUUCGCACUCC 456 1326
UCUAGACUCGUGGUGGACU 1656 1327
GCUGCUAUGCCUCAUCUUC 1824 1328
AGUCUAGACUCGUGGUGGA 1654 1329
CUCCUCUGCCGAUCCAUAC 2662 1330
UGGCUCAGUUUACUAGUGC 2077 1331
GUCUAGACUCGUGGUGGAC 1655 1332
UUCAAGCCUCCAAGCUGUG 51 1333
CUAUGGGAGUGGGCCUCAG 2047 1334
CUCGUGGUGGACUUCUCUC 1662 1335
CCUAUGGGAGUGGGCCUCA 2046 1336
AAGAACUCCCUCGCCUCGC 568 1337
UCUGCCGAUCCAUACUGCG 2666 1338
AGAGUCUAGACUCGUGGUG 1652 1339
GAAGAAGAACUCCCUCGCC 564 1340
UCAAGCCUCCAAGCUGUGC 52 1341
AGCCUCCAAGCUGUGCCUU 55 1342
129
Target Sequence Target Site SEQ ID NO:
AGACUCGUGGUGGACUUCU 1659 1343
Table 13. Various HBV siNA sense and antisense sequences corresponding to the identified target sequences in Table la. (Activity data and exemplary Chemical modifications available at WO2012/024170, incorporated herein by reference)
Target Site SEQID NO: Sense Sequence Antisense Sequence SEQID NO:
1663 1344 UCGUGGUGGACUUCUCUCA UGAGAGAAGUCCACCACGA 1395
1665 1345 GUGGUGGACUUCUCUCAAU AUUGAGAGAAGUCCACCAC 1396
2669 1346 GCCGAUCCAUACUGCGGAA UUCCGCAGUAUGGAUCGGC 1397
2670 1347 CCGAUCCAUACUGCGGAAC GUUCCGCAGUAUGGAUCGG 1398
1818 1348 CAUCCUGCUGCUAUGCCUC GAGGCAUAGCAGCAGGAUG 1399
1823 1349 UGCUGCUAUGCCUCAUCUU AAGAUGAGGCAUAGCAGCA 1400
1667 1350 GGUGGACUUCUCUCAAUUU AAAUUGAGAGAAGUCCACC 1401
1666 1351 UGGUGGACUUCUCUCAAUU AAUUGAGAGAAGUCCACCA 1402
1658 1352 UAGACUCGUGGUGGACUUC GAAGUCCACCACGAGUCUA 1403
2663 1353 UCCUCUGCCGAUCCAUACU AGUAUGGAUCGGCAGAGGA 1404
2668 1354 UGCCGAUCCAUACUGCGGA UCCGCAGUAUGGAUCGGCA 1405
1783 1355 UGGAUGUGUCUGCGGCGUU AACGCCGCAGACACAUCCA 1406
2671 1356 CGAUCCAUACUGCGGAACU AGUUCCGCAGUAUGGAUCG 1407
2934 1357 CGCACCUCUCUUUACGCGG CCGCGUAAAGAGAGGUGCG 1408
2667 1358 CUGCCGAUCCAUACUGCGG CCGCAGUAUGGAUCGGCAG 1409
1664 1359 CGUGGUGGACUUCUCUCAA UUGAGAGAAGUCCACCACG 1410
1822 1360 CUGCUGCUAUGCCUCAUCU AGAUGAGGCAUAGCAGCAG 1411
1821 1361 CCUGCUGCUAUGCCUCAUC GAUGAGGCAUAGCAGCAGG 1412
1657 1362 CUAGACUCGUGGUGGACUU AAGUCCACCACGAGUCUAG 1413
1820 1363 UCCUGCUGCUAUGCCUCAU AUGAGGCAUAGCAGCAGGA 1414
1660 1364 GACUCGUGGUGGACUUCUC GAGAAGUCCACCACGAGUC 1415
130
Target Site SEQID NO: Sense Sequence Antisense Sequence SEQID NO:
2673 1365 AUCCAUACUGCGGAACUCC GGAGUUCCGCAGUAUGGAU 1416
2665 1366 CUCUGCCGAUCCAUACUGC GCAGUAUGGAUCGGCAGAG 1417
2672 1367 GAUCCAUACUGCGGAACUC GAGUUCCGCAGUAUGGAUC 1418
567 1368 GAAGAACUCCCUCGCCUCG CGAGGCGAGGGAGUUCUUC 1419
54 1369 AAGCCUCCAAGCUGUGCCU AGGCACAGCUUGGAGGCUU 1420
566 1370 AGAAGAACUCCCUCGCCUC GAGGCGAGGGAGUUCUUCU 1421
455 1371 GGAGUGUGGAUUCGCACUC GAGUGCGAAUCCACACUCC 1422
2664 1372 CCUCUGCCGAUCCAUACUG CAGUAUGGAUCGGCAGAGG 1423
53 1373 CAAGCCUCCAAGCUGUGCC GGCACAGCUUGGAGGCUUG 1424
2674 1374 UCCAUACUGCGGAACUCCU AGGAGUUCCGCAGUAUGGA 1425
1651 1375 CAGAGUCUAGACUCGUGGU ACCACGAGUCUAGACUCUG 1426
565 1376 AAGAAGAACUCCCUCGCCU AGGCGAGGGAGUUCUUCUU 1427
456 1377 GAGUGUGGAUUCGCACUCC GGAGUGCGAAUCCACACUC 1428
1656 1378 UCUAGACUCGUGGUGGACU AGUCCACCACGAGUCUAGA 1429
1824 1379 GCUGCUAUGCCUCAUCUUC GAAGAUGAGGCAUAGCAGC 1430
1654 1380 AGUCUAGACUCGUGGUGGA UCCACCACGAGUCUAGACU 1431
2662 1381 CUCCUCUGCCGAUCCAUAC GUAUGGAUCGGCAGAGGAG 1432
2077 1382 UGGCUCAGUUUACUAGUGC GCACUAGUAAACUGAGCCA 1433
1655 1383 GUCUAGACUCGUGGUGGAC GUCCACCACGAGUCUAGAC 1434
51 1384 UUCAAGCCUCCAAGCUGUG CACAGCUUGGAGGCUUGAA 1435
2047 1385 CUAUGGGAGUGGGCCUCAG CUGAGGCCCACUCCCAUAG 1436
1662 1386 CUCGUGGUGGACUUCUCUC GAGAGAAGUCCACCACGAG 1437
2046 1387 CCUAUGGGAGUGGGCCUCA UGAGGCCCACUCCCAUAGG 1438
568 1388 AAGAACUCCCUCGCCUCGC GCGAGGCGAGGGAGUUCUU 1439
2666 1389 UCUGCCGAUCCAUACUGCG CGCAGUAUGGAUCGGCAGA 1440
1652 1390 AGAGUCUAGACUCGUGGUG CACCACGAGUCUAGACUCU 1441
564 1391 GAAGAAGAACUCCCUCGCC GGCGAGGGAGUUCUUCUUC 1442
131
Target Site SEQID NO: Sense Sequence Antisense Sequence SEQID NO:
52 1392 UCAAGCCUCCAAGCUGUGC GCACAGCUUGGAGGCUUGA 1443
55 1393 AGCCUCCAAGCUGUGCCUU AAGGCACAGCUUGGAGGCU 1444
1659 1394 AGACUCGUGGUGGACUUCU AGAAGUCCACCACGAGUCU 1445
132
EQUIVALENTS
Those skilled in the art will recognize, or be able to ascertain using no more than routine expérimentation, many équivalents to the spécifie embodiments and methods described herein. Such équivalents are intended to be encompassed by the scope of the following claims.

Claims (47)

1. An RNAi agent, a protein-based HBV vaccine, and a nucleic acid-based HBV vaccine for use in treatment of hepatitis B virus (HBV) infection, wherein:
a) the RNAi agent inhibits expression of at least three HBV transcripts, and comprises a sense strand and an antisense strand forming a double stranded région;
b) the protein-based HBV vaccine comprises a first HBV core antigen (HBeAg) polypeptide, or immunogenic fragment thereof, and a first HBV surface antigen (HBsAg) polypeptide, or immunogenic fragment thereof;
c) the nucleic acid-based HBV vaccine comprising an expression vector construct encoding a second HBeAg polypeptide, or immunogenic fragment thereof, and/or a second HBsAg polypeptide, or immunogenic fragment thereof; .
d) the second HBeAg polypeptide, or immunogenic fragment thereof, and/or the second HBsAg polypeptide, or immunogenic fragment thereof, shares at least one epitope with at least one of the first HBeAg polypeptide, or immunogenic fragment thereof, and/or the first HBsAg polypeptide, or immunogenic fragment thereof; and (e ) the RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine is for sequential administration to a subject having an HBV infection.
2. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of claim 1 or the use of claim 47, wherein the nucleic acid-based HBV vaccine comprises an expression vector construct encoding the second HBeAg polypeptide, or immunogenic fragment thereof, and the second HBsAg polypeptide, or immunogenic fragment thereof.
3. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of claim 1 or 2 or the use of claim 2 or 47, wherein (a) the RNAi agent is for administration to the subject such that the level of HBsAg in the sérum of the subject is decreased, and administration decreases the level of HBsAg in the sérum of the subject, by at least 0.5 log 10 HJ/ml; (b) the level of HBsAg in the sérum of the subject is decreased by at least a 0.5 logIO lU/ml, at least a 1 logIO lU/ml, or at least a 2 log 10 lU/ml prior to administration of a first dose of the protein-based HBV vaccine; (c) the level of HBeAg in the sérum of the subject is decreased by at least a 1 log 10 lU/ml prior to administration of a first dose ofthe protein-based HBV vaccine; (d) the level of HBsAg in the sérum ofthe subject is decreased by at least a 2 log 10 lU/ml and the level ofHBeAg in the sérum ofthe subject is decreased by at least a 1 log 10 lU/ml prior to administration of a first dose ofthe protein based vaccine; (e) the subject has a sérum HBsAg level of 500 lU/ml or less, 200 HJ/ml or less, or 100 lU/ml or less after administration of the RNAi agent and prior to administration of a first dose of the protein-based HBV vaccine; (I) the subject has a sérum HBeAg level of 500 lU/ml or less, 200 lU/ml or less, or 100 lU/ml or less after administration of the RNAi agent and prior to administration
134 of a first dose of the protein-based HBV vaccine; (g) the level of sérum HBsAg in the subject is below 3000 lU/ml, 4000 lU/ml, or 5000 lU/ml prior to administration of the RNAi agent; (h) the level of sérum HBsAg in the subject is decreased to below the level of détection using a clinical assay for at least six months after the end of the dose of the nucleic acid-based HBV vaccine; (i) the level of sérum HBeAg in the subject is decreased to below the level of détection using a clinical assay for at least six months after the end of the dose of the nucleic acid-based HBV vaccine; (j) the level of sérum HBeAg in the subject is decreased to below the level of détection using a clinical assay for at least six months after the end of the dose of the nucleic acid-based HBV vaccine; or (k) the level of sérum HBsAg and HBeAg in the subject are decreased to below the level of détection using a clinical assay for at least six months after the end of the dose of the nucleic acid-based HBV vaccine.
4. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-3 or the use of any one of claims 2-3 and 47, wherein (a) the RNAi agent is for administration in at least two doses to the subject; or (b) the RNAi agent is for administration to the subject in one dose no more than once per week or no more than once every four weeks.
5. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-4 or the use of any claims 2-4 and 47, wherein the RNAi agent is to be administered to the subject at a dose of 0.01 mg/kg to 10 mg/kg; 0.5 mg/kg to 50 mg/kg; 10 mg/kg to 30 mg/kg; 0.5 mg/kg; 1 mg/kg; 1.5 mg/kg; 3 mg/kg; 5 mg/kg; 10 mg/kg; or 30 mg/kg.
6. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-5 or the use of any one of claims 2-5 and 47, wherein the first HBeAg polypeptide, or immunogenic fragment thereof, comprises at least one HBeAg déterminant and the first HBsAg polypeptide, or immunogenic fragment thereof, comprises at least one HBsAg déterminant.
7. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-6 or the use of any one of claims 2-6 and 47, wherein the second HBeAg polypeptide, or immunogenic fragment thereof, comprises at least one HBeAg déterminant and the second HBsAg polypeptide, or immunogenic fragment thereof, comprises at least one HBsAg déterminant.
8. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 6 or 7, wherein the first and/or second HBsAg déterminant comprises an amino acid sequence at least 90% identical to amino acids 124 to 147 of SEQ ID NO: 22; or an amino acid sequence at least 90% identical to amino acids 99 to 168 of SEQ ID NO: 23.
135
9. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 6 or 7, wherein the first and/or second HBcAg déterminant comprises: an amino acid sequence comprising amino acid residue 80 of SEQ ID NO: 24; an amino acid sequence at least 90% identical to at least amino acids 70 to 90 of SEQ ID NO: 24; an amino acid sequence comprising amino acid residue 138 of SEQ ID NO: 24; an amino acid sequence at least 90% identical to at least amino acids 128 to 143 of SEQ ID NO: 24; an amino acid sequence at least 90% identical to at least 40, 50, 60, 70, 80, 90, or 100 contiguous amino acids of SEQ ID NO: 24; or an amino acid sequence at least 90% identical to amino acids 18 to 143 of SEQ ID NO: 24.
10. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-9 or the use of any one of claims 2-9 and 47, wherein the protein-based HBV vaccine is to be administered to the subject at a dose of about 0.1 pg to about 1.0 mg of the first HBcAg polypeptide, or immunogenic fragment thereof, and a dose of about 0.1 pg to about 1.0 mg of the first HBsAg polypeptide, or immunogenic fragment thereof.
11. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any of claims 1-10 or the use of any one of claims 2-10 and 47, wherein the protein-based HBV vaccine further comprises an adjuvant.
12. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 11, wherein the adjuvant is monophosphoryl lipid A (MPL), poly(I:C), polyICLC adjuvant, CpG DNA, polyICLC adjuvant, a STING agonist, c-di-AMP, c-diGMP, c-di-CMP; short, blunt-ended 5'-triphosphate dsRNA (3pRNA) Rig-Iligand, poly[di(sodiumcarboxylatoethylphenoxy)phosphazene] (PCEP)), alum, virosomes, cytokines, IL-12, AS02, AS03, AS04, MF59, ISCOMATRIX®, IC31®, or Rig-I ligand.
13. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-12 or the use of any one of claims 2-11 and 47, wherein a dose of the protein-based HBV vaccine is to be administered to the subject: at least two times; no more than once every two weeks; no sooner than the day on which a final dose ofthe RNAi agent has been administered to the subject; on the same day as a final dose of the RNAi agent has been administered to the subject; no later than one month after a final dose of the RNAi agent has been administered to the subject; or no later than three months after a final dose of the RNAi agent has been administered to the subject.
14. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-13 or the use of any one of claims 2-13 and 47, wherein the
136 nucleic acid-based HBV vaccine comprises at least one expression vector construct encoding the second HBeAg polypeptide, or immunogenic fragment thereof, and the second HBsAg polypeptide, or immunogenic fragment thereof.
15. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 14, wherein the at least one expression construct comprises (a) a promoter that promotes expression of the second HBeAg polypeptide, or immunogenic fragment thereof, and the second HBsAg polypeptide, or immunogenic fragment thereof; or (b) a first and second promoter, the first promoter promoting expression of the second HBeAg polypeptide, or immunogenic fragment thereof, and the second promoter promoting expression of the second HBsAg polypeptide, or immunogenic fragment thereof.
16. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 15 wherein at least one the promoters is selected from the group consisting of a respiratory syncytial virus (RSV) promoter, a cytomégalovirus (CMV) promoter, a PH5 promoter, and an H1 promoter.
17. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any of claims 1-16 or the use of any one of claims 2-16 and 47, wherein the expression construct comprises a viral vector.
18. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 17, wherein the viral vector is selected from the group consisting of an adenovirus vector; a retrovirus vector, a lentiviral vector, a moloney murine leukemia virus vector, an adeno- associated virus vector; a herpes simplex virus vector; a SV 40 vector; a polyoma virus vector; a papilloma virus vector; a picomavirus vector; a pox virus vector, an orthopox virus vector, a vaccinia virus vector, a modified vaccinia virus Ankara (MVA) vector, an avipox vector, a canary pox vector, a fowl pox vector, and an Epstein Barr virus vector.
19. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-18 or the use of any one of claims 2-18 and 47, wherein the nucleic acid-based HBV vaccine is to be administered to the subject at a tissue-culture infectious dose (TCIDjo) of 106 to 10'° TCIDjo; or 106 to 109 TCID50; or 106 to 108 TCID50.
20. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-19 or the use of any one of claims 2-18 and 47, wherein (a) a dose of the nucleic acid-based HBV vaccine is to be administered to the subject no sooner than two weeks after administration of a final dose of the protein-based vaccine is administered to the subject;
137 (b) a first dose of the nucleic acid-based HBV vaccine is to be administered to the subject when the level of HBsAg in the sérum of the subject is further decreased to at least 0.5 log 10 lU/ml following administration of at least one dose of the protein-based HBV vaccine; or (c) a single dose of the nucleic acid-based HBV vaccine is administered to the subject.
21. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-20 or the use of any one of claims 2-20 and 47, for coadministration with, or wherein the composition is for co-administration with, a nucleot(s)ide analog to the subject.
22. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 21, wherein at least one dose of the nucleot(s)ide analog is to be administered to the subject prior to administration of the RNAi agent to the subject; or multiple doses of the nucleot(s)ide analog are to be administered to the subject.
23. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 21 or 22, wherein the nucleot(s)ide analog is Tenofovir disoproxil fumarate (TDF), Tenofovir alafenamide (TAF), Lamivudine, Adefovir dipivoxil, Entecavir (ETV), Telbivudine, AGX-1009, emtricitabine, clcvudinc, ritonavir, dipivoxil, lobucavir, famvir, FTC, NAcetyl-Cysteine (NAC), PC1323, theradigm-HBV, thymosin-alpha, and ganciclovir, besifovir (ANA380/LB-80380), or tenofvir-exaliades (TLX/CMX157).
24. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-23 or the use of any one of claims 2-23 and 47, for coadministration with, or wherein the composition is for co-administration with, an immune stimulator to the subject.
25. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 24, wherein immune stimulator is pegylated interferon alfa 2a (PEG-lFN-alpha-2a), Interferon alfa-2b, PEG-IFN-alpha-2b, Interferon lambda a recombinant human interleukin-7, and a Toll-like receptor 3, 7, 8 or 9 (TLR3, TLR7, TLR8, TLR9) agonist, a viral entry inhibitor, Myrcludex, an oligonucleotide that inhibits the sécrétion or release of HBsAg, REP 9AC, a capsid inhibitor, Bay41-4109, NVR-1221, a cccDNA inhibitor, IHVR-25) a viral capsid, an MVA capsid, an immune checkpoint regulator, an CTLA-4 inhibitor, ipilimumab, a PD-1 inhibitor, Nivolumab, Pembrolizumab, BGB-A317 antibody, a PD-L1 inhibitor, atezolizumab, avelumab, durvalumab, or an affimer biotherapeutic.
138 * . .
26. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-25 or the use of any one of claims 2-25 and 47, wherein the subject is human.
5
27. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-26 or the use of any one of claims 2-26 and 47, wherein the RNAi agent inhibits expression of four HBV transcripts or at least three HBV transcripts.
28. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV 10 vaccine for use of any one of claims 1 -27 or the use of any one of claims 2-27 and 47, wherein the RNAi agent is selected from any one of the iRNA agents in Appendix A.
29. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-28 or the use of any one of claims 2-28 and 47, wherein the 15 RNAi agent targets at least 15 contiguous nucléotides of nucléotides 1579-1597, 206-228,207-229, 210-232,212-234, 214-236, 215-237,216-238,226-248, 245-267,250-272,252-274, 253-275, 254276, 256-278, 258-280, 263-285, 370-392, 373-395,375-397,401-423,405-427,410-432,411-433, 422-444,424-446, 425-447, 426-448, 731-753, 734-756, 1174-1196, 1250-1272, 1255-1277, 12561278, 1545-1567, 1547-1569, 1551-1571, 1577-1597, 1580-1598, 1806-1825, 1812-1831, 1814-1836, 20 1829-1851, 1831-1853, 1857-1879, 1864-1886,2259-2281, 2298-2320, or 2828-2850 ofSEQID
NO: 1 (NC_003977.1).
30. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-29 or the use of any one of claims 2-29 and 47, wherein the 25 RNAi agent targets at least 15 contiguous nucléotides of nucléotides 1579-1597 or 1812-1831 of SEQ ID NO: 1 (NC_003977.1).
31. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 29, wherein the antisense strand of the RNAi agent comprises at 30 least 15 contiguous nucléotides of the nucléotide sequence of 5’UGUGAAGCGAAGUGCACACUU-3’ (SEQ ID NO: 25) or 5’AGGUGAAAAAGUUGCAUGGUGUU-3’ (SEQ ID NO: 26).
32. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV 35 vaccine for use or the use of claim 29, wherein the antisense strand of the RNAi agent comprises the nucléotide sequence of 5’-UGUGAAGCGAAGUGCACACUU-3’ (SEQ ID NO: 25) or 5’AGGUGAAAAAGUUGCAUGGUGUU-3’ (SEQ ID NO: 26).
139
33. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of any one of claims 29-32, wherein the sense strand of the RNAi agent comprises at least 15 contiguous nucléotides of the nucléotide sequence of 5’GUGUGCACUUCGCUUCACA-3’ (SEQ ID NO: 27) or 5’-CACCAUGCAACUUUUUCACCU-3’ (SEQ ID NO: 28).
34. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of any one of claims 29-32, wherein the sense strand of the RNAi agent comprises the nucléotide sequence of 5’-GUGUGCACUUCGCUUCACA-3’ (SEQ ID NO: 27) or 5’CACCAUGCAACUUUUUCACCU-3’ (SEQ ID NO: 28).
35. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 29 or 30, wherein the antisense strand of the RNAi agent comprises at least 15 contiguous nucléotides of the nucléotide sequence of 5’UGUGAAGCGAAGUGCACACUU-3’ (SEQ ID NO: 25) and the sense strand comprises at least 15 contiguous nucléotides of the nucléotide sequence of 5’-GUGUGCACUUCGCUUCACA-3’ (SEQ ID NO: 27).
36. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 29 or 30, wherein the antisense strand of the RNAi agent comprises the nucléotide sequence of 5’-UGUGAAGCGAAGUGCACACUU-3’ (SEQ ID NO: 25) and the sense strand comprises the nucléotide sequence of 5’-GUGUGCACUUCGCUUCACA-3’ (SEQ ID NO: 27).
37. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 29 or 30, wherein the antisense strand of the RNAi agent comprises at least 15 contiguous nucléotides of the nucléotide sequence of 5’AGGUGAAAAAGUUGCAUGGUGUU-3’ (SEQ ID NO: 26) and the sense strand of the RNAi agent comprises at least 15 contiguous nucléotides of the nucléotide sequence of 5’CACCAUGCAACUUUUUCACCU-3 ’ (SEQ ID NO: 28).
38. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 29 or 30, wherein the antisense strand of the RNAi agent comprises the nucléotide sequence of 5’-AGGUGAAAAAGUUGCAUGGUGUU-3’ (SEQ ID NO: 26) and the sense strand of the RNAi agent comprises the nucléotide sequence of 5’CACCAUGCAACUUUUUCACCU-3’ (SEQ ID NO: 28).
140
39. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any one of claims 1-38 or the use of any one of claims 2-38 and 47, wherein (a) the RNAi agent comprises at least one modified nucléotide;
(b) substantially ail of the nucléotides of said sense strand and substantially ail of the nucléotides of said antisense strand are modified nucléotides, wherein said sense strand is conjugated to a ligand attached at the 3’-terminus;
(c) the RNAi agent comprises a 3’ overhang of at least 1 nucléotide or at least 2 nucléotides;
(d) the double-stranded région of the RNAi agent is 15-30,17-23,17-25,23-27,19-21, or 2123 nucléotide pairs in length; or (e) each strand of the RNAi agent has 15-30 or 19-30 nucléotides.
40. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 39, wherein the ligand is one or more GalNAc dérivatives attached through a monovalent linker, bivalent branched linker, or trivalent branched linker.
41. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 40, wherein at least one of said modified nucléotides is a deoxynucleotide, a 3’-terminaI deoxy-thymine (dT) nucléotide, a2'-O-methyl modifiednucléotide, a2fluoro modified nucléotide, a 2'-deoxy-modified nucléotide, a locked nucléotide, an unlocked nucléotide, a conformationally restricted nucléotide, a constrained ethyl nucléotide, an abasic nucléotide, a 2’-amino-modified nucléotide, a 2’-O-allyl-modified nucléotide, 2’-C-alkyl-modified nucléotide, 2’-hydroxly-modified nucléotide, a 2’-methoxyethyl modified nucléotide, a 2’-O-alkylmodified nucléotide, a morpholino nucléotide, a phosphoramidate, a non-natural base comprising nucléotide, a tetrahydropyran modified nucléotide, a 1,5-anhydrohexitol modified nucléotide, a cyclohexenyl modified nucléotide, a nucléotide comprising a phosphorothioate group, a nucléotide comprising a methylphosphonate group, a nucléotide comprising a 5’-phosphate, or a nucléotide comprising a 5’-phosphate mimic.
42. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 39, wherein the ligand is
141
43. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use or the use of claim 39, wherein the RNAi agent is conjugated to the ligand as shown in
5 the following schematic
wherein X is O or S.
44. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV
10 vaccine for use of any of claims 1 -29 or the use of any one of claims 2-29 and 47 wherein the RNAi agent is AD-66810 or AD-66816.
45. The RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine for use of any of claims 1 -44 or the use of any one of claims 2-44 and 47, wherein the first or
15 second HBeAg polypeptide, or immunogenic fragment thereof, and/or the first or second HBsAg polypeptide, or immunogenic fragment thereof, comprise at least one déterminant présent in at least four, at least six, or at least seven génotypes of HBV.
46. A kit for treating a subject having an HBV infection, the kit comprising:
20 a) an RNAi agent that inhibits expression of at least three HBV transcripts, wherein the RNAi agent comprises a sense strand and an antisense strand forming a double stranded région;
142
b) a protein-based vaccine comprising a first HBV core antigen (HBeAg) polypeptide, or immunogenic fragment thereof, and a first HBV surface antigen (HBsAg) polypeptide, or immunogenic fragment thereof; and
c) a nucleic acid-based vaccine comprising an expression vector construct encoding a second
5 HBeAg polypeptide, or immunogenic fragment thereof, and/or a second HBsAg polypeptide, or immunogenic fragment thereof, wherein the second HBeAg polypeptide, or immunogenic fragment thereof, and/or the second HBsAg polypeptide, or immunogenic fragment thereof, shares at least one epitope with at least one of the first HBeAg polypeptide, or immunogenic fragment thereof, and/or the first HBsAg polypeptide, 10 or immunogenic fragment thereof; and
d) instructions for use according to the uses of any one of claims 1-45.
47. Use of an RNAi agent, a protein-based HBV vaccine, and a nucleic acid-based HBV vaccine in the manufacture of a pharmaceutical composition for treating hepatitis B virus (HBV) 15 infection, wherein
a) the RNAi agent inhibits expression of at least three HBV transcripts, and comprises a sense strand and an antisense strand forming a double stranded région;
b) the protein-based HBV vaccine comprises a first HBV core antigen (HBeAg) polypeptide, or immunogenic fragment thereof, and a first HBV surface antigen (HBsAg) polypeptide, or
20 immunogenic fragment thereof;
c) the nucleic acid-based HBV vaccine comprising an expression vector construct encoding a second HBeAg polypeptide, or immunogenic fragment thereof, and/or a second HBsAg polypeptide, or immunogenic fragment thereof;
d) the second HBeAg polypeptide, or immunogenic fragment thereof, and/or the second
25 HBsAg polypeptide, or immunogenic fragment thereof, shares at least one epitope with at least one of the first HBeAg polypeptide, or immunogenic fragment thereof, and/or the first HBsAg polypeptide, or immunogenic fragment thereof; and (e) the RNAi agent, the protein-based HBV vaccine, and the nucleic acid-based HBV vaccine is for sequential administration to a subject having an HBV infection.
OA1201900408 2017-04-18 2018-04-18 Methods for the treatment of subjects having a hepatitis B virus (HBV) infection. OA19808A (en)

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