USOO85O145OB2 (12) United States Patent (10) Patent No.: US 8,501450 B2 Lin et al. (45) Date of Patent: Aug. 6, 2013 (54) HEPATITIS CVIRUS VARIANTS (56) References Cited (75) Inventors: Chao Lin, Winchester, MA (US); Tara U.S. PATENT DOCUMENTS Kieffer, Brookline, MA (US); 4,835,168 A 5/1989 Paget, Jr. et al. Christoph Sarrazin, Saarland (DE); 5,484.801 A 1/1996 Al-RaZZak et al. Ann Kwong, Cambridge, MA (US) 5,631,128 A 5/1997 Kozal et al. 5,807,876 A 9, 1998 Armistead et al. 5,866,684 A 2f1999 Attwood et al. (73) Assignee: Vertex Pharmaceuticals Incorporated, 5.948,436 A 9, 1999 Al-Razzak et al. Cambridge, MA (US) 5.990,276 A 1 1/1999 Zhang et al. 6,018,020 A 1/2000 Attwood et al. (*) Notice: Subject to any disclaimer, the term of this 6,037,157 A 3/2000 Norbeck et al. patent is extended or adjusted under 35 6,054,472 A 4/2000 Armistead et al. U.S.C. 154(b) by 521 days. (Continued) (21) Appl. No.: 12/718,340 FOREIGN PATENT DOCUMENTS WO WO92fO3918 A1 3, 1992 (22) Filed: Mar. 5, 2010 WO WO94f1443.6 A1 T 1994 (65) Prior Publication Data (Continued) US 2011/0244549 A1 Oct. 6, 2011 OTHER PUBLICATIONS Timm, J., et al., 2007. “Human leukocyte antigen-associated Related U.S. Application Data sequence polymorphisms in Hepatitis C Virus reveal reproducible (62) Division of application No. 1 1/599,162, filed on Nov. immune responses and constraints on viral evolution'. Hepatology, 13, 2006, now Pat. No. 7,705,138. vol. 46, pp. 339-349.* (60) Provisional application No. 60/854,598, filed on Oct. (Continued) 25, 2006, provisional application No. 60/735,577, filed on Nov. 11, 2005. Primary Examiner — Manjunath Rao (51) Int. Cl. Assistant Examiner — William W. Moore CI2N 9/50 (2006.01) (74) Attorney, Agent, or Firm — Ropes & Gray LLP CI 2N 15/51 (2006.01) CI 2N 15/57 (2006.01) (57) ABSTRACT CI 2N 15/74 (2006.01) CI 2N 15/79 (2006.01) The present invention relates to HCV variants, particularly CI2P 19/34 (2006.01) variants that are resistant to a protease inhibitors such as (52) U.S. Cl. VX-950. Also provided are methods and compositions USPC ..................... 435/219; 435/252.3:435/320.1; related to the HCV variants. Further provided are methods of 536/23.2:536/23.72 isolating, identifying, and characterizing multiple viral vari (58) Field of Classification Search ants from a patient. None See application file for complete search history. 13 Claims, 33 Drawing Sheets R155 Substitutions Confer Low-level Resistance to Telaprevir Replicon ICs 10 1. o 1 /tatutu u ult R(WT) K T s M N-N-1 Residue 155 US 8,501450 B2 Page 2 U.S. PATENT DOCUMENTS WO WOOO. 59929 A1 10, 2000 6,127.422 A 10/2000 Colacino et al. W8 W88-39. A 658. 6,162,613 A 12/2000 Su et al. WO WOO 1/74768 A2 10, 2001 6,258,558 B1 7/2001 SZostalk et al. WO WOO1,77113 A2 10, 2001 6,265.380 B1 7/2001 Tung et al. WO WO 01/81325 A2 11/2001 6,344,465 B1 2, 2002 Armistead et al. WO WOO2,081.87 A1 1, 2002 6,361,943 B1 3/2002 Yanagawa et al. WO WOO2,08198 A2 1, 2002 6,489,098 B1 12/2002 Petropoulos et al. WO WOO2,08244 A2 1, 2002 6,498,178 B2 12/2002 Stamos et al. WO WOO2,082.56 A2 1, 2002 6,538,126 B1 3/2003 Cho et al. WO WO O2, 18369 A2 3, 2002 6,541,496 B1 4/2003 Armistead et al. WO WO O2/48116 A2 6, 2002 6,608,027 B1 8/2003 Tsantrizos et al. WO WOO2.48157 A2 6, 2002 6,617, 130 B1 9/2003 Bogosian et al. WO WO O2/O60926 A2 8, 2002 6,617,156 B1 9/2003 Doucette-Stamm et al. WO WO O2/O68933 A2 9, 2002 6,838.475 B2 1/2005 Arasappan et al. WO WO O2/O79234 A1 10, 2002 6,846,802 B2 1/2005 Chen et al. WO WO 03/00649.0 A1 1, 2003 6,849,254 B1 2/2005 Brass et al. WO WO-03.014381 2, 2003 6,911,428 B2 6/2005 Zhu et al. WO WO 2004/03997O A1 5, 2004 6,914,122 B2 7/2005 Venkatraman et al. WO WO 2004/072243 A2 8, 2004 6,924.270 B2 8/2005 Ganguly et al. WO WO-2005/O125O2 A2 2/2005 6,962.932 B2 11/2005 Blume et al. WO WO 2005/042570 5, 2005 7,208,309 B2 4/2007 Kukoljet al. WO WO 2006, 112482 A1 10, 2006 7,705,138 B2 4/2010 Lin et al. WO WO 2007/031867 A2 3, 2007 2002fOO16294 A1 2, 2002 Venkatraman et al. 2002fOO16442 A1 2, 2002 Llinas-brunet et al. OTHER PUBLICATIONS 2002fOO32175 A1 3/2002 Tung et al. 3:32:3: A. 29: (i. i al. Yi, M., et al., 2006, "Mutations Conferring Resistance to SCH6, a 2003, OOO8828 A1 1/2003 Priestleyrestley et al. Novel Hepatitis C Virus NS3/4A Protease Inhibitor'.1.%d The Journal of 2003/0162169 A1 8/2003 Pellerinet al. Biological Chemistry, vol. 281, No. 12, pp. 8205-8215.* 2003/0207861 A1 1 1/2003 Arasappan et al. Zhou et al., Phenotypic Characterization of Resistant Val Variants 2003/0216325 A1 1 1/2003 Saksena et al. of Hepatitis C Virus NS3-4A Serine Protease, Antimicrobial Agents 38-66. A. 1298 E. al and Chemotherapy, 52(1): 110-120 (2008). 2004/0077600 A1 4/2004 TungK. etC. al.a. 31(Albertietal. 4. “NaturalO) alhistory history of hepatitis C.”C.J. Journal l of HepatolHepatology, 2004/O142876 A1 7/2004 Colarusso et al. & . y 2004/O147483 A1 7/2004 Priestley Alteretal, "The epidemiology of viral hepatitis in the United States, 2004/0214994 A1 10, 2004 Burioni et al. Gastroenterology Clinics of North America, 23(3):437-455 (1994). 2005/0059606 A1 3/2005 Saksena et al. Alter et al., “Recovery, persistence, and sequelae in hepatitis C virus 2005, 0080017 A1 4, 2005 Cottrell et al. infection: a perspective on long-term outcome' Seminars in Liver 2005/0O85425 A1 4/2005 Chen et al. Disease, 2001): 17-35 (2000). 2005/01073042005/0090450 A1 4/20055, 2005 BrittFarmer et al.et al. Alter, “Hepatitis C virus infection in the United States,” Journal of 2005/01 19168 A1 6/2005 Venkatraman et al. Hepatology, 31(1):88-91 (1999). 2005. O136400 A1 6, 2005 Lin et al. Barbato et al., “The solution structure of the N-terminal proteinase 2005.0143439 A1 6, 2005 Blume et al. domain of the hepatitis C virus (HCV) NS3 protein provides new 2005/O153900 A1 7/2005 Velazquez et al. insights into its activation and catalytic mechanism.” Journal of 2005, 0164.921 A1 7/2005 Njoroge et al. Molecular Biology, 289(2):371-384 (1999). 2005/0176648 A1 8/2005 Saksena et al. Bartenschlager et al., "Complex formation between the NS3 serine 2005/0197301 A1 9/2005 Njoroge et al. type proteinase of the hepatitis C virus and NS4A and its importance 2005/0209164 A1 9/2005 Bogen et al. for polyprotein maturation.” Journal of Virology, 69(12):7519-7528 2005/0222047 A1 10, 2005 Chen et al. (1995). S.E.s A. 38 Saga al. Bartenschlager et al., “Kinetic and structural analyses of hepatitis C 2007/029284.0 A1 12/2007 LemonJOroge et et al. al. is brotein processing.”-- - 9 Journal of Virology, 68(8):5045-5055 2009, 0215869 A1 8/2009 Sallberg Bartenschlager et al., “Nonstructural protein 3 of the hepatitis C virus FOREIGN PATENT DOCUMENTS encodes a serine-type proteinase required for cleavage at the N53/4 and N54/5 junctions.” Journal of Virology, 67(7):3835-3844 (1993). W. W. 239, A. 3E Behrens et al., “Identification and properties of the RNA-dependent WO WO 97/40O28 A1 10, 1997 RNA polymerase of hepatitis C virus.” The EMBO.Journal, 15(1): 12 WO WO97/.43310 A1 11, 1997 22 (1996). WO WO 98.11134 A1 3, 1998 Beyer et al., Effect of naturally occurring active site mutations on WO WO 98.12308 A1 3, 1998 hepatitis C virus NS3 protease specificity.” Proteins, 43(2):82-88 WO WO98, 17679 A1 4f1998 (2001). WO WO 98.22496 A2 5, 1998 Blight et al., “Efficient initiation of HCV RNA replication in cell WO WO 98.40381 A1 9, 1998 culture.” Science, 290(5498): 1972-1974 (2000). WO WO 98,46630 A1 10, 1998 Blight et al., “Molecular virology of hepatitis C virus: an update with WO WO99,07733 A2 2, 1999 respect to potential antiviral targets.” Antiviral Therapy, 3(3):71-81 WO WO99,07734 A2 2, 1999 (1998). WO WO99,38888 A2 8, 1999 Casbarra et al., “The effect of prime-site occupancy on the hepatitis WO WO99.5O230 A1 10, 1999 s WO WO99,64442 A1 12/1999 38, NS3 protease structure.” Protein Science, 11(9):2102-2112 WO WOOO/O1718 A2 1, 2000 WO WOOO.09543 A2 2, 2000 Chambers et al., "Evidence that the N-terminal domain of WO WOOOO9558 A1 2, 2000 nonstructural protein NS3 fromyellow fever virus is a serine protease WO WOOO.31129 A1 6, 2000 responsible for site-specific cleavages in the viral polyprotein.” WO WOOO,56331 A1 9, 2000 PNAS, 87(22):8898-8902 (1990). US 8,501450 B2 Page 3 Chander et al., “Treatment of chronic hepatitis C: a systematic Johnson et al., “Update of the Drug Resistance Mutations in HIV-1: review.” Hepatology, 36 (5 Suppl 1):S135-S144 (2002).