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Volumn 52, Issue 15, 2009, Pages 4820-4837

Inhibitors of the hepatitis C virus NS3 protease with basic amine functionality at the P3-amino acid N-terminus: Discovery and optimization of a new series of P2-P4 macrocycles

Author keywords

[No Author keywords available]

Indexed keywords

7 CYCLOHEXYL 4 [[1 [(CYCLOPROPYLSULFONYL)CARBAMOYL] 2 ETHENYLCYCLOPROPYL]CARBAMOYL] 23 METHOXY 6 OXO 3,4,6,7,8,9,10,11,12,13 DECAHYDRO 2H 16,18 ETHENO 2,5 METHANOPYRIDO[3,2 R][1,5,8]OXADIAZACYCLONONADECIN 8 IUM TRIFLUOROACETATE; ACETIC ACID DERIVATIVE; AMINE; AMINO ACID; ANTIVIRUS AGENT; BENZENE DERIVATIVE; CILUPREVIR; CYCLOPROPANE DERIVATIVE; FLUORINE DERIVATIVE; MACROCYCLIC COMPOUND; NONSTRUCTURAL PROTEIN 3; PROTEINASE INHIBITOR; SULFONE DERIVATIVE; TRIPEPTIDE; UNCLASSIFIED DRUG;

EID: 68549135158     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm900372w     Document Type: Article
Times cited : (17)

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    • No effort was made to assign the absolute stereochemistry of the diastereoisomers of the ring closing products 10c-e. In all cases the first diastereoisomers of 10c-e eluted during RP-HPLC purification gave rise to the more active inhibitors. Compounds 13a, 17a, and 18a showed 7- to 89-fold improved enzyme inhibition over 13b, 17b, and 18b, respectively. On the basis of our expectation that (12R)-stereochemistry is favorable for interaction with NS3 (see Results and Discussion in main text for compounds 12a and 12b; note the change of Cahn-Ingold-Prelog priorities for the nonfluorinated analogues 13, 17, and 18, the first eluted isomers of 10c-e (as well as compounds derived from these intermediates) are depicted and named as the (12R)-diastereoisomers
    • No effort was made to assign the absolute stereochemistry of the diastereoisomers of the ring closing products 10c-e. In all cases the first diastereoisomers of 10c-e eluted during RP-HPLC purification gave rise to the more active inhibitors. Compounds 13a, 17a, and 18a showed 7- to 89-fold improved enzyme inhibition over 13b, 17b, and 18b, respectively. On the basis of our expectation that (12R)-stereochemistry is favorable for interaction with NS3 (see Results and Discussion in main text for compounds 12a and 12b; note the change of Cahn-Ingold-Prelog priorities for the nonfluorinated analogues 13, 17, and 18), the first eluted isomers of 10c-e (as well as compounds derived from these intermediates) are depicted and named as the (12R)-diastereoisomers.
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    • NOESY experiments were performed in DMSO-d6 at 600 MHz and 294 K with mixing times varying from 100 to 200 ms. Interproton distances were estimated using the isolated spin-pair approximation (calibration performed on the geminal protons of the vinyl group in P1, NOE intensities were classified as strong, medium, or weak and compared to distances generated by molecular modeling analysis Monte Carlo simulation, For compound 16, modeling clearly indicated different conformational preferences for the proline amide bond of the R- or S-trifluoromethylglycine analogues; the Z-amide is preferred for the 10-R epimer, while the E-amide is preferred for the 10-S. NOESY experiments detected two strong NOEs betweenH10 and both H24/24′, while no NOE was detected between H 10 and H7. These results are consistent only with Z-conformation around the proline amide bond and support R-configurat
    • 10.
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    • Compounds 35a,b were available through routine protecting group changes from intermediates described in the following published patent application: Rosenquist, A.; Thorstensson, F.; Johansson, P.-O.; Kvarnstrom, I.; Ayesa, S.; Classon, B.; Rakos, L.; Samuelsson, B. HCV NS-3 Serine Protease Inhibitors. WO 2005/073216, 2005.
    • Compounds 35a,b were available through routine protecting group changes from intermediates described in the following published patent application: Rosenquist, A.; Thorstensson, F.; Johansson, P.-O.; Kvarnstrom, I.; Ayesa, S.; Classon, B.; Rakos, L.; Samuelsson, B. HCV NS-3 Serine Protease Inhibitors. WO 2005/073216, 2005.
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    • Venkatraman, S.; Bogen, S. L.; Arasappan, A.; Bennett, F.; Chen, K.; Jao, E.; Liu, Y.-T.; Lovey, R.; Hendrata, S.; Huang, Y.; Pan, W.; Parekh, T.; Pinto, P.; Popov, V.; Pike, R.; Ruan, S.; Santhanam, B.; Vibulbhan, B.; Wu, W.; Yang, W.; Kong, J.; Liang, X.; Wong, J.; Liu, R.; Butkiewicz, N.; Chase, R.; Hart, A.; Agrawal, S.; Ingravallo, P.; Pichardo, J.; Kong, R.; Baroudy, B.; Malcolm, B.; Guo, Z.; Prongay, A.; Madison, V.; Broske, L.; Cui, X.; Cheng, K.-C.; Hsieh, Y.; Brisson, J.-M.; Prelusky, D.; Korfmacher, W.; White, R.; Bogdanowich-Knipp, S.; Pavlovsky, A.; Bradley, P.; Saksena, A. K.; Ganguly, A.; Piwinski, J.; Girijavallabhan, V.; Njoroge, F. G. Discovery of (1R,5S)-N-[3- Amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3-[2(S)-[[[(1, 1-dimethylethyl)amino]carbonyl] amino]-3,3-dimethyl-1-oxobutyl]-6,6-dimethyl-3- azabicyclo-[3.1.0]hexan-2(S)-carboxamide (SCH 503034), a Selective, Potent, Orally Bioavailable Hepatitis C Virus NS3 Protease Inhibitor: A Potential Therapeutic Agent for the Treatment of Hepatitis C Infection. J. Med. Chem. 2006, 49, 6074-6086.
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    • For a review on macrocyclic inhibitors of HCV NS3 protease, see the following: Venkatraman, S.; Njoroge, F. G. Macrocyclic Inhibitors of HCV NS3-4A Protease: Design and Structure Activity Relationship. Curr. Top. Med. Chem. 2007, 7, 1290-1301.
    • For a review on macrocyclic inhibitors of HCV NS3 protease, see the following: Venkatraman, S.; Njoroge, F. G. Macrocyclic Inhibitors of HCV NS3-4A Protease: Design and Structure Activity Relationship. Curr. Top. Med. Chem. 2007, 7, 1290-1301.
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    • Occasional reports of tripeptide-like inhibitors of the HCV NS3 protease in which the P3-N atom is uncapped (and/or is basic) have appeared in the patent literature, e.g., WO2005/051410. During the preparation of this manuscript two relevant patent applications appeared: WO2008/070733 reports a series of P1-P3 macrocyclic inhibitors containing a basic P3-N atom; WO2008/060927 reports a series of acyclic tripeptide analogues that feature aromatic or heteroaromatic P3-capping groups.
    • Occasional reports of tripeptide-like inhibitors of the HCV NS3 protease in which the P3-N atom is uncapped (and/or is basic) have appeared in the patent literature, e.g., WO2005/051410. During the preparation of this manuscript two relevant patent applications appeared: WO2008/070733 reports a series of P1-P3 macrocyclic inhibitors containing a basic P3-N atom; WO2008/060927 reports a series of acyclic tripeptide analogues that feature aromatic or heteroaromatic P3-capping groups.
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    • The conformational analysis of 12a and 12b was performed in the absence of the protein using Macromodel and MMFFs as implemented in Maestro7.5. Low energy conformations were sampled, and the backbone atoms of each were first superimposed to a covalent inhibitor from a cocrystal structure and subsequently minimized.
    • The conformational analysis of 12a and 12b was performed in the absence of the protein using Macromodel and MMFFs as implemented in Maestro7.5. Low energy conformations were sampled, and the backbone atoms of each were first superimposed to a covalent inhibitor from a cocrystal structure and subsequently minimized.
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    • Full details of this compound class will be published elsewhere. McCauley, J. A.; McIntyre, C. M.; Rudd, M. T.; Nguyen, K. T.; Romano, J. J.; Butcher, J. W.; Gilbert, K. F.; Bush, K. J.; Holloway, K.; Swestock, J.; Wan, B.-L.; Carroll, S. S.; DiMuzio, J. M.; Graham, D. J.; Ludmerer, S. W.; Mao, S.-S.; Stahlhut, M. W.; Fandozzi, C. M.; Trainor, N.; Olsen, D. B.; Vacca, J. P.; Liverton, N. J. Discovery and Characterisation of MK-7009, a Macrocyclic HepatitisCNS3/4a Protease Inhibitor. Manuscript in preparation.
    • Full details of this compound class will be published elsewhere. McCauley, J. A.; McIntyre, C. M.; Rudd, M. T.; Nguyen, K. T.; Romano, J. J.; Butcher, J. W.; Gilbert, K. F.; Bush, K. J.; Holloway, K.; Swestock, J.; Wan, B.-L.; Carroll, S. S.; DiMuzio, J. M.; Graham, D. J.; Ludmerer, S. W.; Mao, S.-S.; Stahlhut, M. W.; Fandozzi, C. M.; Trainor, N.; Olsen, D. B.; Vacca, J. P.; Liverton, N. J. Discovery and Characterisation of MK-7009, a Macrocyclic HepatitisCNS3/4a Protease Inhibitor. Manuscript in preparation.
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    • For further examples in which cell-based potency is notably enhanced by generation of zwitterionic inhibitors, see the following. Ikegashira, K, Oka, T, Hirashima, S, Noji, S, Yamanaka, H, Hara, Y, Adachi, T, Tsuruha; Doi, S, Hase, Y, Noguchi, T, Ando, I, Ogura, N, Ikeda, S, Hashimoto, H. Discovery of Conformationally Constrained Tetracyclic Compounds as Potent Hepatitis C Virus NS5B RNA Polymerase Inhibitors. J. Med. Chem. 2006, 49, 6950 and references therein
    • For further examples in which cell-based potency is notably enhanced by generation of zwitterionic inhibitors, see the following. Ikegashira, K.; Oka, T.; Hirashima, S.; Noji, S.; Yamanaka, H.; Hara, Y.; Adachi, T.; Tsuruha; Doi, S.; Hase, Y.; Noguchi, T.; Ando, I.; Ogura, N.; Ikeda, S.; Hashimoto, H. Discovery of Conformationally Constrained Tetracyclic Compounds as Potent Hepatitis C Virus NS5B RNA Polymerase Inhibitors. J. Med. Chem. 2006, 49, 6950 and references therein .
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    • The evaluation of rat liver concentrations 4 h postdose is based on liver time-course studies from previous work see ref 10b, Plasma T max values for all compounds reported are below 4 h and are typically in the 0.5-1 h time range
    • max values for all compounds reported are below 4 h and are typically in the 0.5-1 h time range.
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