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Volumn 5, Issue , 2014, Pages

A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations

Author keywords

[No Author keywords available]

Indexed keywords

ASUNAPREVIR; DANOPREVIR; PROTEASE ACTIVATED RNA POLYMERASE; PROTEINASE; RIFAMPICIN; RNA POLYMERASE; UNCLASSIFIED DRUG; ISOQUINOLINE DERIVATIVE; LACTAM; PEPTIDE HYDROLASE; PROTEINASE INHIBITOR; SULFONAMIDE; VIRAL PROTEIN;

EID: 84923266286     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6352     Document Type: Article
Times cited : (80)

References (50)
  • 1
    • 44949142150 scopus 로고    scopus 로고
    • Proteome-derived database-searchable peptide libraries for identifying protease cleavage sites
    • Schilling, O. & Overall, C. M. Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat. Biotechnol. 26, 685-694 (2008).
    • (2008) Nat. Biotechnol. , vol.26 , pp. 685-694
    • Schilling, O.1    Overall, C.M.2
  • 2
    • 33746163862 scopus 로고    scopus 로고
    • Biopharmaceutical benchmarks 2006
    • Walsh, G. Biopharmaceutical benchmarks 2006. Nat. Biotechnol. 24, 769-776 (2006).
    • (2006) Nat. Biotechnol. , vol.24 , pp. 769-776
    • Walsh, G.1
  • 3
    • 33751217186 scopus 로고    scopus 로고
    • Monitoring regulated protein-protein interactions using split TEV
    • Wehr, M. C. et al. Monitoring regulated protein-protein interactions using split TEV. Nat. Methods 3, 985-993 (2006).
    • (2006) Nat. Methods , vol.3 , pp. 985-993
    • Wehr, M.C.1
  • 5
    • 77955620283 scopus 로고    scopus 로고
    • Activation of specific apoptotic caspases with an engineered small-molecule-activated protease
    • Gray, D. C., Mahrus, S. & Wells, J. A. Activation of specific apoptotic caspases with an engineered small-molecule-activated protease. Cell 142, 637-646 (2010).
    • (2010) Cell , vol.142 , pp. 637-646
    • Gray, D.C.1    Mahrus, S.2    Wells, J.A.3
  • 7
    • 0037350545 scopus 로고    scopus 로고
    • Immunotherapy: Past, present and future
    • Waldmann, T. A. Immunotherapy: past, present and future. Nat. Med. 9, 269-277 (2003).
    • (2003) Nat. Med. , vol.9 , pp. 269-277
    • Waldmann T. ., A.1
  • 8
    • 77955331645 scopus 로고    scopus 로고
    • Design of next-generation protein therapeutics
    • Caravella, J. & Lugovskoy, A. Design of next-generation protein therapeutics. Curr. Opin. Chem. Biol. 14, 520-528 (2010).
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , pp. 520-528
    • Caravella, J.1    Lugovskoy, A.2
  • 9
    • 0023646665 scopus 로고
    • Rational modification of enzyme catalysis by engineering surface charge
    • Russell, A. J. & Fersht, A. R. Rational modification of enzyme catalysis by engineering surface charge. Nature 328, 496-500 (1987).
    • (1987) Nature , vol.328 , pp. 496-500
    • Russell, A.J.1    Fersht, A.R.2
  • 10
    • 18744388856 scopus 로고    scopus 로고
    • Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity
    • Varadarajan, N., Gam, J., Olsen, M. J., Georgiou, G. & Iverson, B. L. Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity. Proc. Natl Acad. Sci. USA 102, 6855-6860 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 6855-6860
    • Varadarajan, N.1    Gam, J.2    Olsen, M.J.3    Georgiou, G.4    Iverson, B.L.5
  • 12
    • 46349100463 scopus 로고    scopus 로고
    • Engineering of protease variants exhibiting altered substrate specificity
    • Sellamuthu, S. et al. Engineering of protease variants exhibiting altered substrate specificity. Biochem. Biophys. Res. Commun. 371, 122-126 (2008).
    • (2008) Biochem. Biophys. Res. Commun. , vol.371 , pp. 122-126
    • Sellamuthu, S.1
  • 13
    • 42249107490 scopus 로고    scopus 로고
    • Highly active and selective endopeptidases with programmed substrate specificities
    • Varadarajan, N., Rodriguez, S., Hwang, B. Y., Georgiou, G. & Iverson, B. L. Highly active and selective endopeptidases with programmed substrate specificities. Nat. Chem. Biol. 4, 290-294 (2008).
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 290-294
    • Varadarajan, N.1    Rodriguez, S.2    Hwang, B.Y.3    Georgiou, G.4    Iverson, B.L.5
  • 14
    • 84876919211 scopus 로고    scopus 로고
    • Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries
    • Yi, L. et al. Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries. Proc. Natl Acad. Sci. USA 110, 7229-7234 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 7229-7234
    • Yi, L.1
  • 15
    • 33845339435 scopus 로고    scopus 로고
    • Protease inhibitors in the clinic
    • Abbenante, G. & Fairlie, D. P. Protease inhibitors in the clinic. Med. Chem. 1, 71-104 (2005).
    • (2005) Med. Chem. , vol.1 , pp. 71-104
    • Abbenante, G.1    Fairlie, D.P.2
  • 16
    • 33748308883 scopus 로고    scopus 로고
    • Targeting proteases: Successes, failures and future prospects
    • Turk, B. Targeting proteases: successes, failures and future prospects. Nat. Rev. Drug Discov. 5, 785-799 (2006).
    • (2006) Nat. Rev. Drug Discov. , vol.5 , pp. 785-799
    • Turk, B.1
  • 17
    • 77953013128 scopus 로고    scopus 로고
    • Rapid emergence of protease inhibitor resistance in hepatitis C virus
    • Rong, L., Dahari, H., Ribeiro, R. M. & Perelson, A. S. Rapid emergence of protease inhibitor resistance in hepatitis C virus. Sci. Transl. Med. 2, 30ra32 (2010).
    • (2010) Sci. Transl. Med. , vol.2 , pp. 30ra32
    • Rong, L.1    Dahari, H.2    Ribeiro, R.M.3    Perelson, A.S.4
  • 18
    • 0029563229 scopus 로고
    • Development of drug resistance to HIV-1 protease inhibitors
    • Ridky, T. & Leis, J. Development of drug resistance to HIV-1 protease inhibitors. J. Biol. Chem. 270, 29621-29623 (1995).
    • (1995) J. Biol. Chem. , vol.270 , pp. 29621-29623
    • Ridky, T.1    Leis, J.2
  • 19
    • 55049134097 scopus 로고    scopus 로고
    • Resilience to resistance of HIV-1 protease inhibitors: Profile of darunavir
    • Lefebvre, E. & Schiffer, C. A. Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir. AIDS Rev. 10, 131-142 (2008).
    • (2008) AIDS Rev. , vol.10 , pp. 131-142
    • Lefebvre, E.1    Schiffer, C.A.2
  • 20
    • 84864602817 scopus 로고    scopus 로고
    • The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors
    • Romano, K. P. et al. The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. PLoS Pathog. 8, e1002832 (2012).
    • (2012) PLoS Pathog. , vol.8 , pp. e1002832
    • Romano, K.P.1
  • 21
    • 84895169891 scopus 로고    scopus 로고
    • Resistance mutations against HCV protease inhibitors and antiviral drug design
    • Shang, L., Lin, K. & Yin, Z. Resistance mutations against HCV protease inhibitors and antiviral drug design. Curr. Pharm. Des. 20, 694-703 (2014).
    • (2014) Curr. Pharm. Des. , vol.20 , pp. 694-703
    • Shang, L.1    Lin, K.2    Yin, Z.3
  • 22
    • 77957965126 scopus 로고    scopus 로고
    • Tracking the evolution of multiple in vitro hepatitis C virus replicon variants under protease inhibitor selection pressure by 454 deep sequencing
    • Verbinnen, T. et al. Tracking the evolution of multiple in vitro hepatitis C virus replicon variants under protease inhibitor selection pressure by 454 deep sequencing. J. Virol. 84, 11124-11133 (2010).
    • (2010) J. Virol. , vol.84 , pp. 11124-11133
    • Verbinnen, T.1
  • 24
    • 0035122917 scopus 로고    scopus 로고
    • Predicting the emergence of antibiotic resistance by directed evolution and structural analysis
    • Orencia, M. C., Yoon, J. S., Ness, J. E., Stemmer, W. P. & Stevens, R. C. Predicting the emergence of antibiotic resistance by directed evolution and structural analysis. Nat. Struct. Biol. 8, 238-242 (2001).
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 238-242
    • Orencia, M.C.1    Yoon, J.S.2    Ness, J.E.3    Stemmer, W.P.4    Stevens, R.C.5
  • 25
    • 79955534060 scopus 로고    scopus 로고
    • A system for the continuous directed evolution of biomolecules
    • Esvelt, K. M., Carlson, J. C. & Liu, D. R. A system for the continuous directed evolution of biomolecules. Nature 472, 499-503 (2011).
    • (2011) Nature , vol.472 , pp. 499-503
    • Esvelt, K.M.1    Carlson, J.C.2    Liu, D.R.3
  • 26
    • 0026520387 scopus 로고
    • Converting trypsin to chymotrypsin: The role of surface loops
    • Hedstrom, L., Szilagyi, L. & Rutter, W. J. Converting trypsin to chymotrypsin: the role of surface loops. Science 255, 1249-1253 (1992).
    • (1992) Science , vol.255 , pp. 1249-1253
    • Hedstrom, L.1    Szilagyi, L.2    Rutter, W.J.3
  • 27
    • 16044364658 scopus 로고    scopus 로고
    • Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide
    • Kim, J. L. et al. Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87, 343-355 (1996).
    • (1996) Cell , vol.87 , pp. 343-355
    • Kim, J.L.1
  • 28
    • 84878427504 scopus 로고    scopus 로고
    • Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution
    • Dickinson, B. C., Leconte, A. M., Allen, B., Esvelt, K. M. & Liu, D. R. Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proc. Natl Acad. Sci. USA 110, 9007-9012 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 9007-9012
    • Dickinson, B.C.1    Leconte, A.M.2    Allen, B.3    Esvelt, K.M.4    Liu, D.R.5
  • 29
    • 84874410798 scopus 로고    scopus 로고
    • A population-based experimental model for protein evolution: Effects of mutation rate and selection stringency on evolutionary outcomes
    • Leconte, A. M. et al. A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes. Biochemistry 52, 1490-1499 (2013).
    • (2013) Biochemistry , vol.52 , pp. 1490-1499
    • Leconte, A.M.1
  • 30
    • 84894101033 scopus 로고    scopus 로고
    • Negative selection and stringency modulation in phage-assisted continuous evolution
    • Carlson, J. C., Badran, A. H., Guggiana-Nilo, D. A. & Liu, D. R. Negative selection and stringency modulation in phage-assisted continuous evolution. Nat. Chem. Biol. 10, 216-222 (2014).
    • (2014) Nat. Chem. Biol. , vol.10 , pp. 216-222
    • Carlson, J.C.1    Badran, A.H.2    Guggiana-Nilo, D.A.3    Liu, D.R.4
  • 31
    • 41349091647 scopus 로고    scopus 로고
    • Design and implementation of three incoherent feed-forward motif based biological concentration sensors
    • Entus, R., Aufderheide, B. & Sauro, H. M. Design and implementation of three incoherent feed-forward motif based biological concentration sensors. Syst. Synth. Biol. 1, 119-128 (2007).
    • (2007) Syst. Synth. Biol. , vol.1 , pp. 119-128
    • Entus, R.1    Aufderheide, B.2    Sauro, H.M.3
  • 32
    • 0032527832 scopus 로고    scopus 로고
    • Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme
    • Jeruzalmi, D. & Steitz, T. A. Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 17, 4101-4113 (1998).
    • (1998) EMBO J. , vol.17 , pp. 4101-4113
    • Jeruzalmi, D.1    Steitz, T.A.2
  • 33
    • 84872044131 scopus 로고    scopus 로고
    • New therapeutic strategies in HCV: Second-generation protease inhibitors
    • Clark, V. C., Peter, J. A. & Nelson, D. R. New therapeutic strategies in HCV: second-generation protease inhibitors. Liver Int. 33(Suppl 1): 80-84 (2013).
    • (2013) Liver Int. , vol.33 , pp. 80-84
    • Clark, V.C.1    Peter, J.A.2    Nelson, D.R.3
  • 34
    • 84881314351 scopus 로고    scopus 로고
    • Novel therapies for hepatitis C - One pill fits all?
    • Manns, M. P. & von Hahn, T. Novel therapies for hepatitis C - one pill fits all? Nat. Rev. Drug Discov. 12, 595-610 (2013).
    • (2013) Nat. Rev. Drug Discov. , vol.12 , pp. 595-610
    • Manns, M.P.1    Von Hahn, T.2
  • 35
    • 84896275496 scopus 로고    scopus 로고
    • Discovery of danoprevir (ITMN-191/R7227), a highly selective and potent inhibitor of hepatitis C virus (HCV) NS3/4A protease
    • Jiang, Y. et al. Discovery of danoprevir (ITMN-191/R7227), a highly selective and potent inhibitor of hepatitis C virus (HCV) NS3/4A protease. J. Med. Chem. 57, 1753-1769 (2014).
    • (2014) J. Med. Chem. , vol.57 , pp. 1753-1769
    • Jiang, Y.1
  • 36
    • 84896292745 scopus 로고    scopus 로고
    • The discovery of asunaprevir (BMS-650032), an orally efficacious NS3 protease inhibitor for the treatment of hepatitis C virus infection
    • Scola, P. M. et al. The discovery of asunaprevir (BMS-650032), an orally efficacious NS3 protease inhibitor for the treatment of hepatitis C virus infection. J. Med. Chem. 57, 1730-1752 (2014).
    • (2014) J. Med. Chem. , vol.57 , pp. 1730-1752
    • Scola, P.M.1
  • 37
    • 84455173090 scopus 로고    scopus 로고
    • Virologic escape during danoprevir (ITMN-191/RG7227) monotherapy is hepatitis C virus subtype dependent and associated with R155K substitution
    • Lim, S. R. et al. Virologic escape during danoprevir (ITMN-191/RG7227) monotherapy is hepatitis C virus subtype dependent and associated with R155K substitution. Antimicrob. Agents Chemother. 56, 271-279 (2012).
    • (2012) Antimicrob. Agents Chemother. , vol.56 , pp. 271-279
    • Lim, S.R.1
  • 38
    • 84862560600 scopus 로고    scopus 로고
    • Resistance analysis of the hepatitis C virus NS3 protease inhibitor asunaprevir
    • McPhee, F. et al. Resistance analysis of the hepatitis C virus NS3 protease inhibitor asunaprevir. Antimicrob. Agents Chemother. 56, 3670-3681 (2012).
    • (2012) Antimicrob. Agents Chemother. , vol.56 , pp. 3670-3681
    • McPhee, F.1
  • 39
    • 84883219967 scopus 로고    scopus 로고
    • Resistance analysis of hepatitis C virus genotype 1 prior treatment null responders receiving daclatasvir and asunaprevir
    • McPhee, F. et al. Resistance analysis of hepatitis C virus genotype 1 prior treatment null responders receiving daclatasvir and asunaprevir. Hepatology 58, 902-911 (2013).
    • (2013) Hepatology , vol.58 , pp. 902-911
    • McPhee, F.1
  • 40
    • 79953733509 scopus 로고    scopus 로고
    • Genotype differences in susceptibility and resistance development of hepatitis C virus to protease inhibitors telaprevir (VX-950) and danoprevir (ITMN-191)
    • Imhof, I. & Simmonds, P. Genotype differences in susceptibility and resistance development of hepatitis C virus to protease inhibitors telaprevir (VX-950) and danoprevir (ITMN-191). Hepatology 53, 1090-1099 (2011).
    • (2011) Hepatology , vol.53 , pp. 1090-1099
    • Imhof, I.1    Simmonds, P.2
  • 41
    • 0035711194 scopus 로고    scopus 로고
    • Tobacco etch virus protease: Mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency
    • Kapust, R. B. et al. Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng. 14, 993-1000 (2001).
    • (2001) Protein Eng. , vol.14 , pp. 993-1000
    • Kapust, R.B.1
  • 42
    • 78650481557 scopus 로고    scopus 로고
    • Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding
    • Romano, K. P., Ali, A., Royer, W. E. & Schiffer, C. A. Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. Proc. Natl Acad. Sci. USA 107, 20986-20991 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 20986-20991
    • Romano, K.P.1    Ali, A.2    Royer, W.E.3    Schiffer, C.A.4
  • 43
    • 0019367342 scopus 로고
    • Escherichia coli K-12 clones that overproduce dam methylase are hypermutable
    • Herman, G. E. & Modrich, P. Escherichia coli K-12 clones that overproduce dam methylase are hypermutable. J. Bacteriol. 145, 644-646 (1981).
    • (1981) J. Bacteriol. , vol.145 , pp. 644-646
    • Herman, G.E.1    Modrich, P.2
  • 44
    • 9244225098 scopus 로고    scopus 로고
    • Mutants in the Exo i motif of Escherichia coli dnaQ: Defective proofreading and inviability due to error catastrophe
    • Fijalkowska, I. J. & Schaaper, R. M. Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe. Proc. Natl Acad. Sci. USA 93, 2856-2861 (1996).
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 2856-2861
    • Fijalkowska, I.J.1    Schaaper, R.M.2
  • 45
    • 3142628359 scopus 로고    scopus 로고
    • Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach
    • Yang, H., Wolff, E., Kim, M., Diep, A. & Miller, J. H. Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach. Mol. Microbiol. 53, 283-295 (2004).
    • (2004) Mol. Microbiol. , vol.53 , pp. 283-295
    • Yang, H.1    Wolff, E.2    Kim, M.3    Diep, A.4    Miller, J.H.5
  • 46
    • 0000612097 scopus 로고
    • Inducibility of a gene product required for UV and chemical mutagenesis in Escherichia coli
    • Bagg, A., Kenyon, C. J. & Walker, G. C. Inducibility of a gene product required for UV and chemical mutagenesis in Escherichia coli. Proc. Natl Acad. Sci. USA 78, 5749-5753 (1981).
    • (1981) Proc. Natl Acad. Sci. USA , vol.78 , pp. 5749-5753
    • Bagg, A.1    Kenyon, C.J.2    Walker, G.C.3
  • 47
    • 0024121565 scopus 로고
    • UmuD mutagenesis protein of Escherichia coli: Overproduction, purification, and cleavage by RecA
    • Burckhardt, S. E., Woodgate, R., Scheuermann, R. H. & Echols, H. UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc. Natl Acad. Sci. USA 85, 1811-1815 (1988).
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 1811-1815
    • Burckhardt, S.E.1    Woodgate, R.2    Scheuermann, R.H.3    Echols, H.4
  • 48
    • 33746629428 scopus 로고    scopus 로고
    • Rep and PriA helicase activities prevent RecA from provoking unnecessary recombination during replication fork repair
    • Mahdi, A. A., Buckman, C., Harris, L. & Lloyd, R. G. Rep and PriA helicase activities prevent RecA from provoking unnecessary recombination during replication fork repair. Genes Dev. 20, 2135-2147 (2006).
    • (2006) Genes Dev. , vol.20 , pp. 2135-2147
    • Mahdi, A.A.1    Buckman, C.2    Harris, L.3    Lloyd, R.G.4
  • 49
    • 84894101033 scopus 로고    scopus 로고
    • Negative selection and stringency modulation enable phage-assisted continuous evolution (PACE) of enzymes with altered specificity
    • Accepted
    • Carlson, J. C., Badran, A. H., Guggiana-Nilo, D. A. & Liu, D. R. Negative selection and stringency modulation enable phage-assisted continuous evolution (PACE) of enzymes with altered specificity. Nat. Chem. Biol. 10, 216-222 Accepted (2013).
    • (2013) Nat. Chem. Biol. , vol.10 , pp. 216-222
    • Carlson, J.C.1    Badran, A.H.2    Guggiana-Nilo, D.A.3    Liu, D.R.4
  • 50
    • 0345549815 scopus 로고
    • A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions
    • Cupples, C. G. & Miller, J. H. A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions. Proc. Natl Acad. Sci. USA 86, 5345-5349 (1989).
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 5345-5349
    • Cupples, C.G.1    Miller, J.H.2


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