Skip to main content

Engineering Therapeutic Enzymes

  • Chapter
  • First Online:
Directed Enzyme Evolution: Advances and Applications

Abstract

Biologics constitute a rapidly growing category of pharmaceutical drug products. With over 100 clinically approved therapeutics and many more in development, protein-based compounds represent an important subset among these biomacromolecular drug candidates, ranging from antibodies, anticoagulants, growth factors, hormones, interferons, and interleukins to enzymes. While recombinant gene technology has traditionally played a key role in development and production of these therapeutics, protein engineering offers an additional dimension for tailoring the biochemical and biophysical properties of proteins to the specific needs of clinical applications. Given the tremendous potential of protein engineering methods to alter and improve the function of biocatalysts, our review focuses on recent examples highlighting the advances and challenges in applying these techniques toward the engineering of therapeutic enzymes. More specifically, our review will focus on three categories of therapeutic enzymes: pharmaceutical enzymes where the protein itself constitutes the therapeutic agent, prodrug-activating enzymes where the protein indirectly triggers a clinical effect, and diagnostic enzymes where a protein’s superior selectivity and specificity offer advantages over traditional analytical methods.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Leader B, Baca QJ, Golan DE (2008) Protein therapeutics: a summary and pharmacological classification. Nat Rev Drug Discov 7(1):21–39

    Article  CAS  PubMed  Google Scholar 

  2. Dimitrov DS (2012) Therapeutic proteins. Methods Mol Biol 899:1–26

    Article  CAS  PubMed  Google Scholar 

  3. Kurtzman AL, Govindarajan S, Vahle K, Jones JT, Heinrichs V, Patten PA (2001) Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins. Curr Opin Biotechnol 12(4):361–370

    Article  CAS  PubMed  Google Scholar 

  4. Vasserot AP, Dickinson CD, Tang Y, Huse WD, Manchester KS, Watkins JD (2003) Optimization of protein therapeutics by directed evolution. Drug Discov Today 8(3):118–126

    Article  CAS  PubMed  Google Scholar 

  5. McCafferty J, Glover DR (2000) Engineering therapeutic proteins. Curr Opin Struct Biol 10(4):417–420

    Article  CAS  PubMed  Google Scholar 

  6. Shak S, Capon DJ, Hellmiss R, Marsters SA, Baker CL (1990) Recombinant human DNase I reduces the viscosity of cystic fibrosis sputum. Proc Natl Acad Sci U S A 87(23):9188–9192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Quan JM, Tiddens HA, Sy JP, McKenzie SG, Montgomery MD, Robinson PJ, Wohl ME, Konstan MW, Pulmozyme Early Intervention Trial Study G (2001) A two-year randomized, placebo-controlled trial of dornase alfa in young patients with cystic fibrosis with mild lung function abnormalities. J Pediatr 139(6):813–820

    Article  CAS  PubMed  Google Scholar 

  8. Corrie PG (2008) Cytotoxic chemotherapy: clinical aspects. Medicine 36(1):24–28

    Article  Google Scholar 

  9. Greco O, Dachs GU (2001) Gene directed enzyme/prodrug therapy of cancer: historical appraisal and future prospectives. J Cell Physiol 187(1):22–36

    Article  CAS  PubMed  Google Scholar 

  10. Moolten FL (1986) Tumor chemosensitivity conferred by inserted herpes thymidine kinase genes: paradigm for a prospective cancer control strategy. Cancer Res 46(10):5276–5281

    CAS  PubMed  Google Scholar 

  11. Encell LP, Landis DM, Loeb LA (1999) Improving enzymes for cancer gene therapy. Nat Biotechnol 17(2):143–147

    Article  CAS  PubMed  Google Scholar 

  12. Duarte S, Carle G, Faneca H, De Lima MCP, Pierrefite-Carle V (2012) Suicide gene therapy in cancer: where do we stand now? Cancer Lett 324(2):160–170

    Article  CAS  PubMed  Google Scholar 

  13. Zarogoulidis, P, Darwiche, K, Sakkas, A, Yarmus, L, Huang, H, Li, Q, Freitag, L, Zarogoulidis, K, Malecki, M (2013) Suicide gene therapy for cancer – current strategies. J Genet Syndr Gene Ther 4 pii:16849

    Google Scholar 

  14. Hamada Y, Kiso Y (2016) New directions for protease inhibitors directed drug discovery. Biopolymers 106(4):563–579

    Article  CAS  PubMed  Google Scholar 

  15. Kurokawa M, Ito T, Yang CS, Zhao C, Macintyre AN, Rizzieri DA, Rathmell JC, Deininger MW, Reya T, Kornbluth S (2013) Engineering a BCR-ABL-activated caspase for the selective elimination of leukemic cells. Proc Natl Acad Sci U S A 110(6):2300–2305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Noppen B, Fonteyn L, Aerts F, De Vriese A, De Maeyer M, Le Floch F, Barbeaux P, Zwaal R, Vanhove M (2014) Autolytic degradation of ocriplasmin: a complex mechanism unraveled by mutational analysis. Protein Eng Des Sel 27(7):215–223

    Article  CAS  PubMed  Google Scholar 

  17. Craik CS, Page MJ, Madison EL (2011) Proteases as therapeutics. Biochem J 435(1):1–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Collen D, Lijnen HR (2009) The tissue-type plasminogen activator story. Arterioscler Thromb Vasc Biol 29(8):1151–1155

    Article  CAS  PubMed  Google Scholar 

  19. Hoylaerts M, Rijken DC, Lijnen HR, Collen D (1982) Kinetics of the activation of plasminogen by human tissue plasminogen activator. Role of fibrin. J Biol Chem 257(6):2912–2919

    CAS  PubMed  Google Scholar 

  20. Andreasen PA, Egelund R, Petersen HH (2000) The plasminogen activation system in tumor growth, invasion, and metastasis. Cell Mol Life Sci 57(1):25–40

    Article  CAS  PubMed  Google Scholar 

  21. Semba CP, Sugimoto K, Razavi MK, Society of C, Interventional R (2001) Alteplase and tenecteplase: applications in the peripheral circulation. Tech Vasc Interv Radiol 4(2):99–106

    Article  CAS  PubMed  Google Scholar 

  22. Keyt BA, Paoni NF, Refino CJ, Berleau L, Nguyen H, Chow A, Lai J, Pena L, Pater C, Ogez J et al (1994) A faster-acting and more potent form of tissue plasminogen activator. Proc Natl Acad Sci U S A 91(9):3670–3674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Bennett WF, Paoni NF, Keyt BA, Botstein D, Jones AJ, Presta L, Wurm FM, Zoller MJ (1991) High resolution analysis of functional determinants on human tissue-type plasminogen activator. J Biol Chem 266(8):5191–5201

    CAS  PubMed  Google Scholar 

  24. Refino CJ, Paoni NF, Keyt BA, Pater CS, Badillo JM, Wurm FM, Ogez J, Bennett WF (1993) A variant of t-PA (T103N, KHRR 296-299 AAAA) that, by bolus, has increased potency and decreased systemic activation of plasminogen. Thromb Haemost 70(2):313–319

    CAS  PubMed  Google Scholar 

  25. Llevadot J, Giugliano RP (2000) Pharmacology and clinical trial results of lanoteplase in acute myocardial infarction. Exp Opin Inv Drugs 9(11):2689–2694

    Article  CAS  Google Scholar 

  26. Lundblad RL, Bradshaw RA, Gabriel D, Ortel TL, Lawson J, Mann KG (2004) A review of the therapeutic uses of thrombin. Thromb Haemost 91(5):851–860

    CAS  PubMed  Google Scholar 

  27. Gibbs CS, Coutre SE, Tsiang M, Li WX, Jain AK, Dunn KE, Law VS, Mao CT, Matsumura SY, Mejza SJ et al (1995) Conversion of thrombin into an anticoagulant by protein engineering. Nature 378(6555):413–416

    Article  CAS  PubMed  Google Scholar 

  28. Tsiang M, Paborsky LR, Li WX, Jain AK, Mao CT, Dunn KE, Lee DW, Matsumura SY, Matteucci MD, Coutre SE, Leung LL, Gibbs CS (1996) Protein engineering thrombin for optimal specificity and potency of anticoagulant activity in vivo. Biochemistry 35(51):16449–16457

    Article  CAS  PubMed  Google Scholar 

  29. Marino F, Pelc LA, Vogt A, Gandhi PS, Di Cera E (2010) Engineering thrombin for selective specificity toward protein C and PAR1. J Biol Chem 285(25):19145–19152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Gruber A, Cantwell AM, Di Cera E, Hanson SR (2002) The thrombin mutant W215A/E217A shows safe and potent anticoagulant and antithrombotic effects in vivo. J Biol Chem 277(31):27581–27584

    Article  CAS  PubMed  Google Scholar 

  31. Berny-Lang MA, Hurst S, Tucker EI, Pelc LA, Wang RK, Hurn PD, Di Cera E, McCarty OJ, Gruber A (2011) Thrombin mutant W215A/E217A treatment improves neurological outcome and reduces cerebral infarct size in a mouse model of ischemic stroke. Stroke 42(6):1736–1741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Arosio D, Ayala YM, Di Cera E (2000) Mutation of W215 compromises thrombin cleavage of fibrinogen, but not of PAR-1 or protein C. Biochemistry 39(27):8095–8101

    Article  CAS  PubMed  Google Scholar 

  33. Persson E, Kjalke M, Olsen OH (2001) Rational design of coagulation factor VIIa variants with substantially increased intrinsic activity. Proc Natl Acad Sci U S A 98(24):13583–13588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lentz SR, Ehrenforth S, Karim FA, Matsushita T, Weldingh KN, Windyga J, Mahlangu JN, adept™2 investigators (2014) Recombinant factor VIIa analog in the management of hemophilia with inhibitors: results from a multicenter, randomized, controlled trial of vatreptacog alfa. J Thromb Haemost 12 (8):1244–1253

    Google Scholar 

  35. Harvey SB, Stone MD, Martinez MB, Nelsestuen GL (2003) Mutagenesis of the gamma-carboxyglutamic acid domain of human factor VII to generate maximum enhancement of the membrane contact site. J Biol Chem 278(10):8363–8369

    Article  CAS  PubMed  Google Scholar 

  36. Neuenschwander PF, Morrissey JH (1994) Roles of the membrane-interactive regions of factor VIIa and tissue factor. The factor VIIa Gla domain is dispensable for binding to tissue factor but important for activation of factor X. J Biol Chem 269(11):8007–8013

    CAS  PubMed  Google Scholar 

  37. Mahlangu J, Paz P, Hardtke M, Aswad F, Schroeder J (2016) TRUST trial: BAY 86-6150 use in haemophilia with inhibitors and assessment for immunogenicity. Haemophilia. doi:10.1111/hae.12994

    Google Scholar 

  38. Qian X, Hamad B, Dias-Lalcaca G (2015) The Alzheimer disease market. Nat Rev Drug Discov 14(10):675–676

    Article  CAS  PubMed  Google Scholar 

  39. Jacobsen JS, Comery TA, Martone RL, Elokdah H, Crandall DL, Oganesian A, Aschmies S, Kirksey Y, Gonzales C, Xu J, Zhou H, Atchison K, Wagner E, Zaleska MM, Das I, Arias RL, Bard J, Riddell D, Gardell SJ, Abou-Gharbia M, Robichaud A, Magolda R, Vlasuk GP, Bjornsson T, Reinhart PH, Pangalos MN (2008) Enhanced clearance of Abeta in brain by sustaining the plasmin proteolysis cascade. Proc Natl Acad Sci U S A 105(25):8754–8759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Leissring MA, Farris W, Chang AY, Walsh DM, Wu X, Sun X, Frosch MP, Selkoe DJ (2003) Enhanced proteolysis of beta-amyloid in APP transgenic mice prevents plaque formation, secondary pathology, and premature death. Neuron 40(6):1087–1093

    Article  CAS  PubMed  Google Scholar 

  41. Spencer B, Marr RA, Rockenstein E, Crews L, Adame A, Potkar R, Patrick C, Gage FH, Verma IM, Masliah E (2008) Long-term neprilysin gene transfer is associated with reduced levels of intracellular Abeta and behavioral improvement in APP transgenic mice. BMC Neurosci 9:109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Sexton T, Hitchcook LJ, Rodgers DW, Bradley LH, Hersh LB (2012) Active site mutations change the cleavage specificity of neprilysin. PLoS One 7(2):e32343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Webster CI, Burrell M, Olsson LL, Fowler SB, Digby S, Sandercock A, Snijder A, Tebbe J, Haupts U, Grudzinska J, Jermutus L, Andersson C (2014) Engineering neprilysin activity and specificity to create a novel therapeutic for Alzheimer’s disease. PLoS One 9(8):e104001

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Eckman EA, Adams SK, Troendle FJ, Stodola BA, Kahn MA, Fauq AH, Xiao HD, Bernstein KE, Eckman CB (2006) Regulation of steady-state beta-amyloid levels in the brain by neprilysin and endothelin-converting enzyme but not angiotensin-converting enzyme. J Biol Chem 281(41):30471–30478

    Article  CAS  PubMed  Google Scholar 

  45. Guerrero JL, O’Malley MA, Daugherty PS (2016) Intracellular FRET-based screen for redesigning the specificity of secreted proteases. ACS Chem Biol 11(4):961–970

    Article  CAS  PubMed  Google Scholar 

  46. Dressler D (2012) Clinical applications of botulinum toxin. Curr Opin Microbiol 15(3):325–336

    Article  PubMed  Google Scholar 

  47. Orsini M, Leite MA, Chung TM, Bocca W, de Souza JA, de Souza OG, Moreira RP, Bastos VH, Teixeira S, Oliveira AB, Moraes Bda S, Matta AP, Jacinto LJ (2015) Botulinum neurotoxin type A in neurology: update. Neurol Int 7(2):5886

    PubMed  PubMed Central  Google Scholar 

  48. Masuyer G, Chaddock JA, Foster KA, Acharya KR (2014) Engineered botulinum neurotoxins as new therapeutics. Annu Rev Pharmacol Toxicol 54:27–51

    Article  CAS  PubMed  Google Scholar 

  49. Vazquez-Cintron E, Tenezaca L, Angeles C, Syngkon A, Liublinska V, Ichtchenko K, Band P (2016) Pre-clinical study of a novel recombinant botulinum neurotoxin derivative engineered for improved safety. Sci Rep 6:30429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Rummel A, Mahrhold S, Bigalke H, Binz T (2011) Exchange of the H(CC) domain mediating double receptor recognition improves the pharmacodynamic properties of botulinum neurotoxin. FEBS J 278(23):4506–4515

    Article  CAS  PubMed  Google Scholar 

  51. Wang J, Zurawski TH, Bodeker MO, Meng J, Boddul S, Aoki KR, Dolly JO (2012) Longer-acting and highly potent chimaeric inhibitors of excessive exocytosis created with domains from botulinum neurotoxin A and B. Biochem J 444(1):59–67

    Article  CAS  PubMed  Google Scholar 

  52. Wang J, Zurawski TH, Meng J, Lawrence G, Olango WM, Finn DP, Wheeler L, Dolly JO (2011) A dileucine in the protease of botulinum toxin A underlies its long-lived neuroparalysis: transfer of longevity to a novel potential therapeutic. J Biol Chem 286(8):6375–6385

    Article  CAS  PubMed  Google Scholar 

  53. Chaddock JA, Purkiss JR, Friis LM, Broadbridge JD, Duggan MJ, Fooks SJ, Shone CC, Quinn CP, Foster KA (2000) Inhibition of vesicular secretion in both neuronal and nonneuronal cells by a retargeted endopeptidase derivative of Clostridium botulinum neurotoxin type A. Infect Immun 68(5):2587–2593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Fonfria E, Donald S, Cadd VA (2016) Botulinum neurotoxin A and an engineered derivate targeted secretion inhibitor (TSI) A enter cells via different vesicular compartments. J Recept Signal Transduct Res 36(1):79–88

    CAS  PubMed  Google Scholar 

  55. Ma H, Meng J, Wang J, Hearty S, Dolly JO, O’Kennedy R (2014) Targeted delivery of a SNARE protease to sensory neurons using a single chain antibody (scFv) against the extracellular domain of P2X(3) inhibits the release of a pain mediator. Biochem J 462(2):247–256

    Article  CAS  PubMed  Google Scholar 

  56. Larsen GR, Timony GA, Horgan PG, Barone KM, Hensen KS, Augus LB, Stoudemire JB (1991) Protein engineering of novel plasminogen activators with increased thrombolytic potency in rabbits relative to activase. J Biol Chem 266(1):8156–8161

    Google Scholar 

  57. Sikorra S, Litschko C, Muller C, Thiel N, Galli T, Eichner T, Binz T (2016) Identification and characterization of botulinum neurotoxin a substrate binding pockets and their re-engineering for human SNAP-23. J Mol Biol 428(2 Pt A):372–384

    Article  CAS  PubMed  Google Scholar 

  58. Chen S, Barbieri JT (2009) Engineering botulinum neurotoxin to extend therapeutic intervention. Proc Natl Acad Sci U S A 106(23):9180–9184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Somm E, Bonnet N, Martinez A, Marks PM, Cadd VA, Elliott M, Toulotte A, Ferrari SL, Rizzoli R, Huppi PS, Harper E, Melmed S, Jones R, Aubert ML (2012) A botulinum toxin-derived targeted secretion inhibitor downregulates the GH/IGF1 axis. J Clin Invest 122(9):3295–3306

    Article  PubMed  PubMed Central  Google Scholar 

  60. Tye-Din JA, Anderson RP, Ffrench RA, Brown GJ, Hodsman P, Siegel M, Botwick W, Shreeniwas R (2010) The effects of ALV003 pre-digestion of gluten on immune response and symptoms in celiac disease in vivo. Clin Immunol 134(3):289–295

    Article  CAS  PubMed  Google Scholar 

  61. Ehren J, Govindarajan S, Moron B, Minshull J, Khosla C (2008) Protein engineering of improved prolyl endopeptidases for celiac sprue therapy. Protein Eng Des Sel 21(12):699–707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel JB (2012) Computational design of an alpha-gliadin peptidase. J Am Chem Soc 134(50):20513–20520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Tack GJ, Verbeek WH, Schreurs MW, Mulder CJ (2010) The spectrum of celiac disease: epidemiology, clinical aspects and treatment. Nat Rev Gastroenterol Hepatol 7(4):204–213

    Article  CAS  PubMed  Google Scholar 

  64. Shan L, Molberg O, Parrot I, Hausch F, Filiz F, Gray GM, Sollid LM, Khosla C (2002) Structural basis for gluten intolerance in celiac sprue. Science 297(5590):2275–2279

    Article  CAS  PubMed  Google Scholar 

  65. Wolf C, Siegel JB, Tinberg C, Camarca A, Gianfrani C, Paski S, Guan R, Montelione G, Baker D, Pultz IS (2015) Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions. J Am Chem Soc 137(40):13106–13113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Guerrero JL, Daugherty PS, O’Malley MA (2016) Emerging technologies for protease engineering: new tools to clear out disease. Biotechnol Bioeng. doi:10.1002/bit.26066 [Epub ahead of print]

    PubMed  Google Scholar 

  67. Esvelt KM, Carlson JC, Liu DR (2011) A system for the continuous directed evolution of biomolecules. Nature 472(7344):499–503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Hill ME, MacPherson DJ, Wu P, Julien O, Wells JA, Hardy JA (2016) Reprogramming caspase-7 specificity by regio-specific mutations and selection provides alternate solutions for substrate recognition. ACS Chem Biol 11(6):1603–1612

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Sandersjoo L, Kostallas G, Lofblom J, Samuelson P (2014) A protease substrate profiling method that links site-specific proteolysis with antibiotic resistance. Biotechnol J 9(1):155–162

    Article  PubMed  CAS  Google Scholar 

  70. Varadarajan N, Rodriguez S, Hwang BY, Georgiou G, Iverson BL (2008) Highly active and selective endopeptidases with programmed substrate specificities. Nat Chem Biol 4(5):290–294

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Kostallas G, Samuelson P (2010) Novel fluorescence-assisted whole-cell assay for engineering and characterization of proteases and their substrates. Appl Environ Microbiol 76(22):7500–7508

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Carrico ZM, Strobel KL, Atreya ME, Clark DS, Francis MB (2016) Simultaneous selection and counter-selection for the directed evolution of proteases in E. coli using a cytoplasmic anchoring strategy. Biotechnol Bioeng 113(6):1187–1193

    Article  CAS  PubMed  Google Scholar 

  73. Dickinson BC, Packer MS, Badran AH, Liu DR (2014) A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations. Nat Commun 5:5352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Ledoux L (1955) Action of ribonuclease on two solid tumours in vivo. Nature 176(4470):36–37

    Article  CAS  PubMed  Google Scholar 

  75. Vogelzang NJ, Aklilu M, Stadler WM, Dumas MC, Mikulski SM (2001) A phase II trial of weekly intravenous ranpirnase (Onconase), a novel ribonuclease in patients with metastatic kidney cancer. Investig New Drugs 19(3):255–260

    Article  CAS  Google Scholar 

  76. Mikulski SM, Costanzi JJ, Vogelzang NJ, McCachren S, Taub RN, Chun H, Mittelman A, Panella T, Puccio C, Fine R, Shogen K (2002) Phase II trial of a single weekly intravenous dose of ranpirnase in patients with unresectable malignant mesothelioma. J Clin Oncol 20(1):274–281

    Article  CAS  PubMed  Google Scholar 

  77. Rutkoski TJ, Raines RT (2008) Evasion of ribonuclease inhibitor as a determinant of ribonuclease cytotoxicity. Curr Pharm Biotechnol 9(3):185–189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Kobe B, Deisenhofer J (1996) Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. J Mol Biol 264(5):1028–1043

    Article  CAS  PubMed  Google Scholar 

  79. Leland PA, Schultz LW, Kim BM, Raines RT (1998) Ribonuclease A variants with potent cytotoxic activity. Proc Natl Acad Sci U S A 95(18):10407–10412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Rutkoski TJ, Kurten EL, Mitchell JC, Raines RT (2005) Disruption of shape-complementarity markers to create cytotoxic variants of ribonuclease A. J Mol Biol 354(1):41–54

    Article  CAS  PubMed  Google Scholar 

  81. Johnson RJ, Chao TY, Lavis LD, Raines RT (2007) Cytotoxic ribonucleases: the dichotomy of Coulombic forces. Biochemistry 46(36):10308–10316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Johnson RJ, McCoy JG, Bingman CA, Phillips GN Jr, Raines RT (2007) Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein. J Mol Biol 368(2):434–449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Cremer C, Braun H, Mladenov R, Schenke L, Cong X, Jost E, Brummendorf TH, Fischer R, Carloni P, Barth S, Nachreiner T (2015) Novel angiogenin mutants with increased cytotoxicity enhance the depletion of pro-inflammatory macrophages and leukemia cells ex vivo. Cancer Immunol Immunother 64(12):1575–1586

    Article  CAS  PubMed  Google Scholar 

  84. Cong X, Cremer C, Nachreiner T, Barth S, Carloni P (2016) Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: insights from enhanced sampling simulations. Protein Sci. doi:10.1002/pro.2941

    PubMed  Google Scholar 

  85. Riccio G, D’Avino C, Raines RT, De Lorenzo C (2013) A novel fully human antitumor immunoRNase resistant to the RNase inhibitor. Protein Eng Des Sel 26(3):243–248

    Article  CAS  PubMed  Google Scholar 

  86. Phillips MM, Sheaff MT, Szlosarek PW (2013) Targeting arginine-dependent cancers with arginine-degrading enzymes: opportunities and challenges. Cancer Res Treat 45(4):251–262

    Article  PubMed  PubMed Central  Google Scholar 

  87. Patil MD, Bhaumik J, Babykutty S, Banerjee UC, Fukumura D (2016) Arginine dependence of tumor cells: targeting a chink in cancer’s armor. Oncogene. doi:10.1038/onc.2016.37

    Google Scholar 

  88. Boissel N, Sender LS (2015) Best practices in adolescent and young adult patients with acute lymphoblastic leukemia: a focus on asparaginase. Young Adult Oncol 4(3):118–128

    Article  Google Scholar 

  89. Pulte D, Gondos A, Brenner H (2009) Improvement in survival in younger patients with acute lymphoblastic leukemia from the 1980s to the early 21st century. Blood 113(7):1408–1411

    Article  CAS  PubMed  Google Scholar 

  90. Liu C, Kawedia JD, Cheng C, Pei D, Fernandez CA, Cai X, Crews KR, Kaste SC, Panetta JC, Bowman WP, Jeha S, Sandlund JT, Evans WE, Pui CH, Relling MV (2012) Clinical utility and implications of asparaginase antibodies in acute lymphoblastic leukemia. Leukemia 26(11):2303–2309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Cantor JR, Yoo TH, Dixit A, Iverson BL, Forsthuber TG, Georgiou G (2011) Therapeutic enzyme deimmunization by combinatorial T-cell epitope removal using neutral drift. Proc Natl Acad Sci U S A 108(4):1272–1277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Maggi M, Chiarelli LR, Valentini G, Scotti C (2015) Engineering of Helicobacter pylori L-asparaginase: characterization of two functionally distinct groups of mutants. PLoS One 10(2):e0117025

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  93. Bansal S, Srivastava A, Mukherjee G, Pandey R, Verma AK, Mishra P, Kundu B (2012) Hyperthermophilic asparaginase mutants with enhanced substrate affinity and antineoplastic activity: structural insights on their mechanism of action. FASEB J 26(3):1161–1171

    Article  CAS  PubMed  Google Scholar 

  94. Kotzia GA, Labrou NE (2009) Engineering thermal stability of L-asparaginase by in vitro directed evolution. FEBS J 276(6):1750–1761

    Article  CAS  PubMed  Google Scholar 

  95. Figueiredo L, Cole PD, Drachtman RA (2016) Asparaginase Erwinia chrysanthemi as a component of a multi-agent chemotherapeutic regimen for the treatment of patients with acute lymphoblastic leukemia who have developed hypersensitivity to E. coli-derived asparaginase. Expert Rev Hematol 9(3):227–234

    Article  CAS  PubMed  Google Scholar 

  96. Feun L, Savaraj N (2006) Pegylated arginine deiminase: a novel anticancer enzyme agent. Expert Opin Investig Drugs 15(7):815–822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Glazer ES, Piccirillo M, Albino V, Di Giacomo R, Palaia R, Mastro AA, Beneduce G, Castello G, De Rosa V, Petrillo A, Ascierto PA, Curley SA, Izzo F (2010) Phase II study of pegylated arginine deiminase for nonresectable and metastatic hepatocellular carcinoma. J Clin Oncol 28(13):2220–2226

    Article  CAS  PubMed  Google Scholar 

  98. Ott PA, Carvajal RD, Pandit-Taskar N, Jungbluth AA, Hoffman EW, Wu BW, Bomalaski JS, Venhaus R, Pan L, Old LJ, Pavlick AC, Wolchok JD (2013) Phase I/II study of pegylated arginine deiminase (ADI-PEG 20) in patients with advanced melanoma. Investig New Drugs 31(2):425–434

    Article  CAS  Google Scholar 

  99. Tomlinson BK, Thomson JA, Bomalaski JS, Diaz M, Akande T, Mahaffey N, Li T, Dutia MP, Kelly K, Gong IY, Semrad T, Gandara DR, Pan CX, Lara PN Jr (2015) Phase I trial of arginine deprivation therapy with ADI-PEG 20 plus docetaxel in patients with advanced malignant solid tumors. Clin Cancer Res 21(11):2480–2486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Liu Y-M, Sun Z-H, Ni Y, Zheng P, Liu Y-P, Meng F-J (2008) Isolation and identification of an arginine deiminase producing strain Pseudomonas plecoglossicida CGMCC2039. World J Microbiol Biotechnol 24(10):2213–2219

    Article  CAS  Google Scholar 

  101. Han RZ, Xu GC, Dong JJ, Ni Y (2016) Arginine deiminase: recent advances in discovery, crystal structure, and protein engineering for improved properties as an anti-tumor drug. Appl Microbiol Biotechnol 100(11):4747–4760

    Article  CAS  PubMed  Google Scholar 

  102. Ni Y, Li Z, Sun Z, Zheng P, Liu Y, Zhu L, Schwaneberg U (2009) Expression of arginine deiminase from Pseudomonas plecoglossicida CGMCC2039 in E. coli and its anti-tumor activity. Curr Microbiol 58(6):593–598

    Article  CAS  PubMed  Google Scholar 

  103. Cheng F, Kardashliev T, Pitzler C, Shehzad A, Lue H, Bernhagen J, Zhu L, Schwaneberg U (2015) A competitive flow cytometry screening system for directed evolution of therapeutic enzyme. ACS Synth Biol 4(7):768–775

    Article  CAS  PubMed  Google Scholar 

  104. Ni Y, Schwaneberg U, Sun ZH (2008) Arginine deiminase, a potential anti-tumor drug. Cancer Lett 261(1):1–11

    Article  CAS  PubMed  Google Scholar 

  105. Kuhn NJ, Talbot J, Ward S (1991) pH-sensitive control of arginase by Mn(II) ions at submicromolar concentrations. Arch Biochem Biophys 286(1):217–221

    Article  CAS  PubMed  Google Scholar 

  106. Stone EM, Glazer ES, Chantranupong L, Cherukuri P, Breece RM, Tierney DL, Curley SA, Iverson BL, Georgiou G (2010) Replacing Mn(2+) with Co(2+) in human arginase i enhances cytotoxicity toward l-arginine auxotrophic cancer cell lines. ACS Chem Biol 5(3):333–342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Stone E, Chantranupong L, Gonzalez C, O’Neal J, Rani M, VanDenBerg C, Georgiou G (2012) Strategies for optimizing the serum persistence of engineered human arginase I for cancer therapy. J Control Release 158(1):171–179

    Google Scholar 

  108. Jordheim LP, Durantel D, Zoulim F, Dumontet C (2013) Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. Nat Rev Drug Discov 12(6):447–464

    Article  CAS  PubMed  Google Scholar 

  109. Baldwin SA, Beal PR, Yao SY, King AE, Cass CE, Young JD (2004) The equilibrative nucleoside transporter family, SLC29. Pflugers Arch 447(5):735–743

    Article  CAS  PubMed  Google Scholar 

  110. Arner ES, Eriksson S (1995) Mammalian deoxyribonucleoside kinases. Pharmacol Ther 67(2):155–186

    Article  CAS  PubMed  Google Scholar 

  111. Shi J, McAtee JJ, Schlueter Wirtz S, Tharnish P, Juodawlkis A, Liotta DC, Schinazi RF (1999) Synthesis and biological evaluation of 2′,3′-didehydro-2′,3′- dideoxy-5-fluorocytidine (D4FC) analogues: discovery of carbocyclic nucleoside triphosphates with potent inhibitory activity against HIV-1 reverse transcriptase. J Med Chem 42(5):859–867

    Article  CAS  PubMed  Google Scholar 

  112. Culver KW, Ram Z, Wallbridge S, Ishii H, Oldfield EH, Blaese RM (1992) In vivo gene transfer with retroviral vector-producer cells for treatment of experimental brain tumors. Science 256(5063):1550–1552

    Article  CAS  PubMed  Google Scholar 

  113. Song S, Pursell ZF, Copeland WC, Longley MJ, Kunkel TA, Mathews CK (2005) DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mutagenesis through reduced replication fidelity. Proc Natl Acad Sci U S A 102(14):4990–4995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Trask TW, Trask RP, Aguilar-Cordova E, Shine HD, Wyde PR, Goodman JC, Hamilton WJ, Rojas-Martinez A, Chen SH, Woo SL, Grossman RG (2000) Phase I study of adenoviral delivery of the HSV-tk gene and ganciclovir administration in patients with current malignant brain tumors. Mol Ther 1(2):195–203

    Article  CAS  PubMed  Google Scholar 

  115. Ji N, Weng D, Liu C, Gu Z, Chen S, Guo Y, Fan Z, Wang X, Chen J, Zhao Y, Zhou J, Wang J, Ma D, Li N (2016) Adenovirus-mediated delivery of herpes simplex virus thymidine kinase administration improves outcome of recurrent high-grade glioma. Oncotarget 7(4):4369–4378

    PubMed  Google Scholar 

  116. Wheeler LA, Manzanera AG, Bell SD, Cavaliere R, McGregor JM, Grecula JC, Newton HB, Lo SS, Badie B, Portnow J, Teh BS, Trask TW, Baskin DS, New PZ, Aguilar LK, Aguilar-Cordova E, Chiocca EA (2016) Phase II multicenter study of gene-mediated cytotoxic immunotherapy as adjuvant to surgical resection for newly diagnosed malignant glioma. Neuro-Oncology 18(8):1137–1145

    Article  PubMed  Google Scholar 

  117. Wigler M, Silverstein S, Lee LS, Pellicer A, Cheng Y, Axel R (1977) Transfer of purified herpes virus thymidine kinase gene to cultured mouse cells. Cell 11(1):223–232

    Article  CAS  PubMed  Google Scholar 

  118. Skorenski M, Sienczyk M (2014) Anti-herpesvirus agents: a patent and literature review (2003 to present). Expert Opin Ther Patents 24(8):925–941

    Article  CAS  Google Scholar 

  119. Munir KM, French DC, Dube DK, Loeb LA (1992) Permissible amino acid substitutions within the putative nucleoside binding site of Herpes Simplex virus type 1 encoded thymidine kinase established by random sequence mutagenesis [corrected]. J Biol Chem 267(10):6584–6589

    CAS  PubMed  Google Scholar 

  120. Black ME, Loeb LA (1993) Identification of important residues within the putative nucleoside binding site of HSV-1 thymidine kinase by random sequence selection: analysis of selected mutants in vitro. Biochemistry 32(43):11618–11626

    Article  CAS  PubMed  Google Scholar 

  121. Black ME, Newcomb TG, Wilson HM, Loeb LA (1996) Creation of drug-specific Herpes Simplex virus type 1 thymidine kinase mutants for gene therapy. Proc Natl Acad Sci U S A 93(8):3525–3529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Christians FC, Scapozza L, Crameri A, Folkers G, Stemmer WP (1999) Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling. Nat Biotechnol 17(3):259–264

    Article  CAS  PubMed  Google Scholar 

  123. Hinds TA, Compadre C, Hurlburt BK, Drake RR (2000) Conservative mutations of glutamine-125 in Herpes Simplex virus type 1 thymidine kinase result in a ganciclovir kinase with minimal deoxypyrimidine kinase activities. Biochemistry 39(14):4105–4111

    Article  CAS  PubMed  Google Scholar 

  124. Black ME, Kokoris MS, Sabo P (2001) Herpes Simplex virus-1 thymidine kinase mutants created by semi-random sequence mutagenesis improve prodrug-mediated tumor cell killing. Cancer Res 61(7):3022–3026

    CAS  PubMed  Google Scholar 

  125. Balzarini J, Liekens S, Solaroli N, El Omari K, Stammers DK, Karlsson A (2006) Engineering of a single conserved amino acid residue of Herpes Simplex virus type 1 thymidine kinase allows a predominant shift from pyrimidine to purine nucleoside phosphorylation. J Biol Chem 281(28):19273–19279

    Article  CAS  PubMed  Google Scholar 

  126. Munch-Petersen B, Piskur J, Sondergaard L (1998) Four deoxynucleoside kinase activities from Drosophila melanogaster are contained within a single monomeric enzyme, a new multifunctional deoxynucleoside kinase. J Biol Chem 273(7):3926–3931

    Article  CAS  PubMed  Google Scholar 

  127. Knecht W, Munch-Petersen B, Piskur J (2000) Identification of residues involved in the specificity and regulation of the highly efficient multisubstrate deoxyribonucleoside kinase from Drosophila melanogaster. J Mol Biol 301(4):827–837

    Article  CAS  PubMed  Google Scholar 

  128. Knecht W, Sandrini MP, Johansson K, Eklund H, Munch-Petersen B, Piskur J (2002) A few amino acid substitutions can convert deoxyribonucleoside kinase specificity from pyrimidines to purines. EMBO J 21(7):1873–1880

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Knecht W, Rozpedowska E, Le Breton C, Willer M, Gojkovic Z, Sandrini MP, Joergensen T, Hasholt L, Munch-Petersen B, Piskur J (2007) Drosophila deoxyribonucleoside kinase mutants with enhanced ability to phosphorylate purine analogs. Gene Ther 14(17):1278–1286

    Article  CAS  PubMed  Google Scholar 

  130. Gerth ML, Lutz S (2007) Non-homologous recombination of deoxyribonucleoside kinases from human and Drosophila melanogaster yields human-like enzymes with novel activities. J Mol Biol 370(4):742–751

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Solaroli N, Johansson M, Balzarini J, Karlsson A (2007) Enhanced toxicity of purine nucleoside analogs in cells expressing Drosophila melanogaster nucleoside kinase mutants. Gene Ther 14(1):86–92

    Article  CAS  PubMed  Google Scholar 

  132. Liu L, Li Y, Liotta D, Lutz S (2009) Directed evolution of an orthogonal nucleoside analog kinase via fluorescence-activated cell sorting. Nucleic Acids Res 37(13):4472–4481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Liu L, Murphy P, Baker D, Lutz S (2010) Computational design of orthogonal nucleoside kinases. Chem Commun (Camb) 46(46):8803–8805

    Article  CAS  Google Scholar 

  134. Campbell DO, Yaghoubi SS, Su Y, Lee JT, Auerbach MS, Herschman H, Satyamurthy N, Czernin J, Lavie A, Radu CG (2012) Structure-guided engineering of human thymidine kinase 2 as a positron emission tomography reporter gene for enhanced phosphorylation of non-natural thymidine analog reporter probe. J Biol Chem 287(1):446–454

    Article  CAS  PubMed  Google Scholar 

  135. Sabini E, Hazra S, Konrad M, Burley SK, Lavie A (2007) Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase. Nucleic Acids Res 35(1):186–192

    Article  CAS  PubMed  Google Scholar 

  136. Iyidogan P, Lutz S (2008) Systematic exploration of active site mutations on human deoxycytidine kinase substrate specificity. Biochemistry 47(16):4711–4720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Hazra S, Sabini E, Ort S, Konrad M, Lavie A (2009) Extending thymidine kinase activity to the catalytic repertoire of human deoxycytidine kinase. Biochemistry 48(6):1256–1263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Muthu P, Chen HX, Lutz S (2014) Redesigning human 2′-deoxycytidine kinase enantioselectivity for L-nucleoside analogues as reporters in positron emission tomography. ACS Chem Biol 9(10):2326–2333

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Kokoris MS, Sabo P, Adman ET, Black ME (1999) Enhancement of tumor ablation by a selected HSV-1 thymidine kinase mutant. Gene Ther 6(8):1415–1426

    Article  CAS  PubMed  Google Scholar 

  140. Ardiani A, Sanchez-Bonilla M, Black ME (2010) Fusion enzymes containing HSV-1 thymidine kinase mutants and guanylate kinase enhance prodrug sensitivity in vitro and in vivo. Cancer Gene Ther 17(2):86–96

    Article  CAS  PubMed  Google Scholar 

  141. Karjoo Z, Chen X, Hatefi A (2016) Progress and problems with the use of suicide genes for targeted cancer therapy. Adv Drug Deliv Rev 99(Pt A):113–128

    Article  CAS  PubMed  Google Scholar 

  142. Balzarini J, Liekens S, Esnouf R, De Clercq E (2002) The A167Y mutation converts the Herpes Simplex virus type 1 thymidine kinase into a guanosine analogue kinase. Biochemistry 41(20):6517–6524

    Article  CAS  PubMed  Google Scholar 

  143. Slot Christiansen L, Munch-Petersen B, Knecht W (2015) Non-viral deoxyribonucleoside kinases – diversity and practical use. J Genet Genomics 42(5):235–248

    Article  PubMed  Google Scholar 

  144. Welin M, Skovgaard T, Knecht W, Zhu C, Berenstein D, Munch-Petersen B, Piskur J, Eklund H (2005) Structural basis for the changed substrate specificity of Drosophila melanogaster deoxyribonucleoside kinase mutant N64D. FEBS J 272(14):3733–3742

    Article  CAS  PubMed  Google Scholar 

  145. Hecker SJ, Erion MD (2008) Prodrugs of phosphates and phosphonates. J Med Chem 51(8):2328–2345

    Article  CAS  PubMed  Google Scholar 

  146. Thornton P, Kadri H, Micolli A, Mehellou Y (2016) Nucleoside phosphate and phosphonate prodrug clinical candidates. J Med Chem. doi:10.1021/acs.jmedchem.6b00523

    PubMed  Google Scholar 

  147. Eriksson S, Kierdaszuk B, Munch-Petersen B, Oberg B, Johansson NG (1991) Comparison of the substrate specificities of human thymidine kinase 1 and 2 and deoxycytidine kinase toward antiviral and cytostatic nucleoside analogs. Biochem Biophys Res Commun 176(2):586–592

    Article  CAS  PubMed  Google Scholar 

  148. Serganova I, Ponomarev V, Blasberg R (2007) Human reporter genes: potential use in clinical studies. Nucl Med Biol 34(7):791–807

    Article  CAS  PubMed  Google Scholar 

  149. Yaghoubi SS, Campbell DO, Radu CG, Czernin J (2012) Positron emission tomography reporter genes and reporter probes: gene and cell therapy applications. Theranostics 2(4):374–391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Gambhir SS, Bauer E, Black ME, Liang Q, Kokoris MS, Barrio JR, Iyer M, Namavari M, Phelps ME, Herschman HR (2000) A mutant Herpes Simplex virus type 1 thymidine kinase reporter gene shows improved sensitivity for imaging reporter gene expression with positron emission tomography. Proc Natl Acad Sci U S A 97(6):2785–2790

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Jacobs A, Tjuvajev JG, Dubrovin M, Akhurst T, Balatoni J, Beattie B, Joshi R, Finn R, Larson SM, Herrlinger U, Pechan PA, Chiocca EA, Breakefield XO, Blasberg RG (2001) Positron emission tomography-based imaging of transgene expression mediated by replication-conditional, oncolytic Herpes Simplex virus type 1 mutant vectors in vivo. Cancer Res 61(7):2983–2995

    CAS  PubMed  Google Scholar 

  152. Dempsey MF, Wyper D, Owens J, Pimlott S, Papanastassiou V, Patterson J, Hadley DM, Nicol A, Rampling R, Brown SM (2006) Assessment of 123I-FIAU imaging of herpes simplex viral gene expression in the treatment of glioma. Nucl Med Commun 27(8):611–617

    Article  PubMed  Google Scholar 

  153. Likar Y, Zurita J, Dobrenkov K, Shenker L, Cai S, Neschadim A, Medin JA, Sadelain M, Hricak H, Ponomarev V (2010) A new pyrimidine-specific reporter gene: a mutated human deoxycytidine kinase suitable for PET during treatment with acycloguanosine-based cytotoxic drugs. J Nucl Med 51(9):1395–1403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Gil JS, Machado HB, Campbell DO, McCracken M, Radu C, Witte ON, Herschman HR (2013) Application of a rapid, simple, and accurate adenovirus-based method to compare PET reporter gene/PET reporter probe systems. Mol Imaging Biol 15(3):273–281

    Article  PubMed  Google Scholar 

  155. Wang L, Munch-Petersen B, Herrstrom Sjoberg A, Hellman U, Bergman T, Jornvall H, Eriksson S (1999) Human thymidine kinase 2: molecular cloning and characterisation of the enzyme activity with antiviral and cytostatic nucleoside substrates. FEBS Lett 443(2):170–174

    Article  CAS  PubMed  Google Scholar 

  156. Ponomarev V, Doubrovin M, Shavrin A, Serganova I, Beresten T, Ageyeva L, Cai C, Balatoni J, Alauddin M, Gelovani J (2007) A human-derived reporter gene for noninvasive imaging in humans: mitochondrial thymidine kinase type 2. J Nucl Med 48(5):819–826

    Article  CAS  PubMed  Google Scholar 

  157. Mullen CA, Kilstrup M, Blaese RM (1992) Transfer of the bacterial gene for cytosine deaminase to mammalian cells confers lethal sensitivity to 5-fluorocytosine: a negative selection system. Proc Natl Acad Sci U S A 89(1):33–37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Mahan SD, Ireton GC, Stoddard BL, Black ME (2004) Alanine-scanning mutagenesis reveals a cytosine deaminase mutant with altered substrate preference. Biochemistry 43(28):8957–8964

    Article  CAS  PubMed  Google Scholar 

  159. Mahan SD, Ireton GC, Knoeber C, Stoddard BL, Black ME (2004) Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy. Protein Eng Des Sel 17(8):625–633

    Article  CAS  PubMed  Google Scholar 

  160. Fuchita M, Ardiani A, Zhao L, Serve K, Stoddard BL, Black ME (2009) Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo. Cancer Res 69(11):4791–4799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Korkegian A, Black ME, Baker D, Stoddard BL (2005) Computational thermostabilization of an enzyme. Science 308(5723):857–860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Stolworthy TS, Korkegian AM, Willmon CL, Ardiani A, Cundiff J, Stoddard BL, Black ME (2008) Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine. J Mol Biol 377(3):854–869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Rogulski KR, Kim JH, Kim SH, Freytag SO (1997) Glioma cells transduced with an Escherichia coli CD/HSV-1 TK fusion gene exhibit enhanced metabolic suicide and radiosensitivity. Hum Gene Ther 8(1):73–85

    Article  CAS  PubMed  Google Scholar 

  164. Chang JW, Lee H, Kim E, Lee Y, Chung SS, Kim JH (2000) Combined antitumor effects of an adenoviral cytosine deaminase/thymidine kinase fusion gene in rat C6 glioma. Neurosurgery 47(4):931–938

    Article  CAS  PubMed  Google Scholar 

  165. Bennett EM, Anand R, Allan PW, Hassan AE, Hong JS, Levasseur DN, McPherson DT, Parker WB, Secrist JA 3rd, Sorscher EJ, Townes TM, Waud WR, Ealick SE (2003) Designer gene therapy using an Escherichia coli purine nucleoside phosphorylase/prodrug system. Chem Biol 10(12):1173–1181

    Article  CAS  PubMed  Google Scholar 

  166. Stoeckler JD, Poirot AF, Smith RM, Parks RE Jr, Ealick SE, Takabayashi K, Erion MD (1997) Purine nucleoside phosphorylase. 3. Reversal of purine base specificity by site-directed mutagenesis. Biochemistry 36(39):11749–11756

    Article  CAS  PubMed  Google Scholar 

  167. Grove JI, Lovering AL, Guise C, Race PR, Wrighton CJ, White SA, Hyde EI, Searle PF (2003) Generation of Escherichia coli nitroreductase mutants conferring improved cell sensitization to the prodrug CB1954. Cancer Res 63(17):5532–5537

    CAS  PubMed  Google Scholar 

  168. Guise CP, Grove JI, Hyde EI, Searle PF (2007) Direct positive selection for improved nitroreductase variants using SOS triggering of bacteriophage lambda lytic cycle. Gene Ther 14(8):690–698

    Article  CAS  PubMed  Google Scholar 

  169. Barak Y, Thorne SH, Ackerley DF, Lynch SV, Contag CH, Matin A (2006) New enzyme for reductive cancer chemotherapy, YieF, and its improvement by directed evolution. Mol Cancer Ther 5(1):97–103

    Article  CAS  PubMed  Google Scholar 

  170. Jaberipour M, Vass SO, Guise CP, Grove JI, Knox RJ, Hu L, Hyde EI, Searle PF (2010) Testing double mutants of the enzyme nitroreductase for enhanced cell sensitisation to prodrugs: effects of combining beneficial single mutations. Biochem Pharmacol 79(2):102–111

    Article  CAS  PubMed  Google Scholar 

  171. Swe PM, Copp JN, Green LK, Guise CP, Mowday AM, Smaill JB, Patterson AV, Ackerley DF (2012) Targeted mutagenesis of the Vibrio fischeri flavin reductase FRase I to improve activation of the anticancer prodrug CB1954. Biochem Pharmacol 84(6):775–783

    Article  CAS  PubMed  Google Scholar 

  172. Bzowska A, Kulikowska E, Shugar D (2000) Purine nucleoside phosphorylases: properties, functions, and clinical aspects. Pharmacol Ther 88(3):349–425

    Article  CAS  PubMed  Google Scholar 

  173. Sorscher EJ, Peng S, Bebok Z, Allan PW, Bennett LL Jr, Parker WB (1994) Tumor cell bystander killing in colonic carcinoma utilizing the Escherichia coli DeoD gene to generate toxic purines. Gene Ther 1(4):233–238

    CAS  PubMed  Google Scholar 

  174. Martiniello-Wilks R, Wang XY, Voeks DJ, Dane A, Shaw JM, Mortensen E, Both GW, Russell PJ (2004) Purine nucleoside phosphorylase and fludarabine phosphate gene-directed enzyme prodrug therapy suppresses primary tumour growth and pseudo-metastases in a mouse model of prostate cancer. J Gene Med 6(12):1343–1357

    Article  CAS  PubMed  Google Scholar 

  175. Lukenbill J, Kalaycio M (2013) Fludarabine: a review of the clear benefits and potential harms. Leuk Res 37(9):986–994

    Article  CAS  PubMed  Google Scholar 

  176. Cacciapuoti G, Bagarolo ML, Martino E, Scafuri B, Marabotti A, Porcelli M (2016) Efficient fludarabine-activating PNP from archaea as a guidance for redesign the active site of E. coli PNP. J Cell Biochem 117(5):1126–1135

    Article  CAS  PubMed  Google Scholar 

  177. Williams EM, Little RF, Mowday AM, Rich MH, Chan-Hyams JV, Copp JN, Smaill JB, Patterson AV, Ackerley DF (2015) Nitroreductase gene-directed enzyme prodrug therapy: insights and advances toward clinical utility. Biochem J 471(2):131–153

    Article  CAS  PubMed  Google Scholar 

  178. Rylott EL, Budarina MV, Barker A, Lorenz A, Strand SE, Bruce NC (2011) Engineering plants for the phytoremediation of RDX in the presence of the co-contaminating explosive TNT. New Phytol 192(2):405–413

    Article  CAS  PubMed  Google Scholar 

  179. White DT, Mumm JS (2013) The nitroreductase system of inducible targeted ablation facilitates cell-specific regenerative studies in zebrafish. Methods 62(3):232–240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Bridgewater J, Springer C, Knox R, Minton N, Michael N, Collins M (1995) Expression of the bacterial nitroreductase enzyme in mammalian cells renders them selectively sensitive to killing by the prodrug CB1954. Eur J Cancer 31(13):2362–2370

    Article  Google Scholar 

  181. Patel P, Young JG, Mautner V, Ashdown D, Bonney S, Pineda RG, Collins SI, Searle PF, Hull D, Peers E, Chester J, Wallace DM, Doherty A, Leung H, Young LS, James ND (2009) A phase I/II clinical trial in localized prostate cancer of an adenovirus expressing nitroreductase with CB1954. Mol Ther 17(7):1292–1299

    Article  CAS  PubMed Central  Google Scholar 

  182. Lovering AL, Hyde EI, Searle PF, White SA (2001) The structure of Escherichia coli nitroreductase complexed with nicotinic acid: three crystal forms at 1.7 A, 1.8 A and 2.4 A resolution. J Mol Biol 309(1):203–213

    Article  CAS  PubMed  Google Scholar 

  183. Vellom DC, Radic Z, Li Y, Pickering NA, Camp S, Taylor P (1993) Amino acid residues controlling acetylcholinesterase and butyrylcholinesterase specificity. Biochemistry 32(1):12–17

    Article  CAS  PubMed  Google Scholar 

  184. Schwarz M, Glick D, Loewenstein Y, Soreq H (1995) Engineering of human cholinesterases explains and predicts diverse consequences of administration of various drugs and poisons. Pharmacol Ther 67(2):283–322

    Article  CAS  PubMed  Google Scholar 

  185. Lockridge O (2015) Review of human butyrylcholinesterase structure, function, genetic variants, history of use in the clinic, and potential therapeutic uses. Pharmacol Ther 148:34–46

    Article  CAS  PubMed  Google Scholar 

  186. Lenz DE, Yeung D, Smith JR, Sweeney RE, Lumley LA, Cerasoli DM (2007) Stoichiometric and catalytic scavengers as protection against nerve agent toxicity: a mini review. Toxicology 233(1–3):31–39

    Article  CAS  PubMed  Google Scholar 

  187. Parikh K, Duysen EG, Snow B, Jensen NS, Manne V, Lockridge O, Chilukuri N (2011) Gene-delivered butyrylcholinesterase is prophylactic against the toxicity of chemical warfare nerve agents and organophosphorus compounds. J Pharmacol Exp Ther 337(1):92–101

    Article  CAS  PubMed  Google Scholar 

  188. Saxena A, Sun W, Fedorko JM, Koplovitz I, Doctor BP (2011) Prophylaxis with human serum butyrylcholinesterase protects guinea pigs exposed to multiple lethal doses of soman or VX. Biochem Pharmacol 81(1):164–169

    Article  CAS  PubMed  Google Scholar 

  189. Terekhov S, Smirnov I, Bobik T, Shamborant O, Zenkova M, Chernolovskaya E, Gladkikh D, Murashev A, Dyachenko I, Palikov V, Palikova Y, Knorre V, Belogurov A Jr, Ponomarenko N, Blackburn GM, Masson P, Gabibov A (2015) A novel expression cassette delivers efficient production of exclusively tetrameric human butyrylcholinesterase with improved pharmacokinetics for protection against organophosphate poisoning. Biochimie 118:51–59

    Article  CAS  PubMed  Google Scholar 

  190. Brimijoin S, Gao Y (2012) Cocaine hydrolase gene therapy for cocaine abuse. Future Med Chem 4(2):151–162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Xie W, Altamirano CV, Bartels CF, Speirs RJ, Cashman JR, Lockridge O (1999) An improved cocaine hydrolase: the A328Y mutant of human butyrylcholinesterase is 4-fold more efficient. Mol Pharmacol 55(1):83–91

    CAS  PubMed  Google Scholar 

  192. Sun H, El Yazal J, Lockridge O, Schopfer LM, Brimijoin S, Pang YP (2001) Predicted Michaelis-Menten complexes of cocaine-butyrylcholinesterase. Engineering effective butyrylcholinesterase mutants for cocaine detoxification. J Biol Chem 276(12):9330–9336

    Article  CAS  PubMed  Google Scholar 

  193. Sun H, Pang YP, Lockridge O, Brimijoin S (2002) Re-engineering butyrylcholinesterase as a cocaine hydrolase. Mol Pharmacol 62(2):220–224

    Article  CAS  PubMed  Google Scholar 

  194. Hamza A, Cho H, Tai HH, Zhan CG (2005) Molecular dynamics simulation of cocaine binding with human butyrylcholinesterase and its mutants. J Phys Chem B 109(10):4776–4782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Gatley SJ (1991) Activities of the enantiomers of cocaine and some related compounds as substrates and inhibitors of plasma butyrylcholinesterase. Biochem Pharmacol 41(8):1249–1254

    Article  CAS  PubMed  Google Scholar 

  196. Pancook JD, Pecht G, Ader M, Mosko M, Lockridge O, Watkins JD (2003) Application of directed evolution technology to optimize the cocaine hydrolase activity of human butyrylcholinesterase. FASEB J 17(4):A565–A565

    Google Scholar 

  197. Pan Y, Gao D, Yang W, Cho H, Yang G, Tai HH, Zhan CG (2005) Computational redesign of human butyrylcholinesterase for anticocaine medication. Proc Natl Acad Sci U S A 102(46):16656–16661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Cohen-Barak O, Wildeman J, van de Wetering J, Hettinga J, Schuilenga-Hut P, Gross A, Clark S, Bassan M, Gilgun-Sherki Y, Mendzelevski B, Spiegelstein O (2015) Safety, pharmacokinetics, and pharmacodynamics of TV-1380, a novel mutated butyrylcholinesterase treatment for cocaine addiction, after single and multiple intramuscular injections in healthy subjects. J Clin Pharmacol 55(5):573–583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Brimijoin S, Gao Y, Anker JJ, Gliddon LA, Lafleur D, Shah R, Zhao Q, Singh M, Carroll ME (2008) A cocaine hydrolase engineered from human butyrylcholinesterase selectively blocks cocaine toxicity and reinstatement of drug seeking in rats. Neuropsychopharmacology 33(11):2715–2725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Chen X, Zheng X, Zhou Z, Zhan CG, Zheng F (2016) Effects of a cocaine hydrolase engineered from human butyrylcholinesterase on metabolic profile of cocaine in rats. Chem Biol Interact. doi:10.1016/j.cbi.2016.05.003

    Google Scholar 

  201. Kim K, Tsay OG, Atwood DA, Churchill DG (2011) Destruction and detection of chemical warfare agents. Chem Rev 111(9):5345–5403

    Article  CAS  PubMed  Google Scholar 

  202. Alder L, Greulich K, Kempe G, Vieth B (2006) Residue analysis of 500 high priority pesticides: better by GC-MS or LC-MS/MS? Mass Spectrom Rev 25(6):838–865

    Article  CAS  PubMed  Google Scholar 

  203. Bhattacharya S, Alsen C, Kruse H, Valentin P (1981) Detection of organo-phosphate insecticide by an immobilized-enzyme system. Environ Sci Technol 15(11):1352–1355

    Article  CAS  Google Scholar 

  204. Razumas VJ, Kulys JJ, Malinauskas AA (1981) High-sensitivity bioamperometric determination of organo-phosphate insecticides. Environ Sci Technol 15(3):360–361

    Article  CAS  PubMed  Google Scholar 

  205. Villatte F, Marcel V, Estrada-Mondaca S, Fournier D (1998) Engineering sensitive acetylcholinesterase for detection of organophosphate and carbamate insecticides. Biosens Bioelectron 13(2):157–164

    Article  CAS  PubMed  Google Scholar 

  206. Boublik Y, Saint-Aguet P, Lougarre A, Arnaud M, Villatte F, Estrada-Mondaca S, Fournier D (2002) Acetylcholinesterase engineering for detection of insecticide residues. Protein Eng 15(1):43–50

    Article  CAS  PubMed  Google Scholar 

  207. Fremaux I, Mazeres S, Brisson-Lougarre A, Arnaud M, Ladurantie C, Fournier D (2002) Improvement of Drosophila acetylcholinesterase stability by elimination of a free cysteine. BMC Biochem 3:21

    Article  PubMed  PubMed Central  Google Scholar 

  208. Schulze H, Muench SB, Villatte F, Schmid RD, Bachmann TT (2005) Insecticide detection through protein engineering of Nippostrongylus brasiliensis acetylcholinesterase B. Anal Chem 77(18):5823–5830

    Article  CAS  PubMed  Google Scholar 

  209. Hussein AS, Chacon MR, Smith AM, Tosado-Acevedo R, Selkirk ME (1999) Cloning, expression, and properties of a nonneuronal secreted acetylcholinesterase from the parasitic nematode Nippostrongylus brasiliensis. J Biol Chem 274(14):9312–9319

    Article  CAS  PubMed  Google Scholar 

  210. Bachmann TT, Schmid RD (1999) A disposable multielectrode biosensor for rapid simultaneous detection of the insecticides paraoxon and carbofuran at high resolution. Anal Chim Acta 401(1–2):95–103

    Article  CAS  Google Scholar 

  211. Bachmann TT, Leca B, Vilatte F, Marty JL, Fournier D, Schmid RD (2000) Improved multianalyte detection of organophosphates and carbamates with disposable multielectrode biosensors using recombinant mutants of Drosophila acetylcholinesterase and artificial neural networks. Biosens Bioelectron 15(3–4):193–201

    Article  CAS  PubMed  Google Scholar 

  212. Vanhooke JL, Benning MM, Raushel FM, Holden HM (1996) Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate. Biochemistry 35(19):6020–6025

    Article  CAS  PubMed  Google Scholar 

  213. Serdar CM, Gibson DT, Munnecke DM, Lancaster JH (1982) Plasmid involvement in parathion hydrolysis by Pseudomonas diminuta. Appl Environ Microbiol 44(1):246–249

    CAS  PubMed  PubMed Central  Google Scholar 

  214. Scanlan TS, Reid RC (1995) Evolution in action. Chem Biol 2(2):71–75

    Article  CAS  PubMed  Google Scholar 

  215. Iyer R, Iken B (2015) Protein engineering of representative hydrolytic enzymes for remediation of organophosphates. Biochem Eng J 94:134–144

    Article  CAS  Google Scholar 

  216. Dumas DP, Durst HD, Landis WG, Raushel FM, Wild JR (1990) Inactivation of organophosphorus nerve agents by the phosphotriesterase from Pseudomonas diminuta. Arch Biochem Biophys 277(1):155–159

    Article  CAS  PubMed  Google Scholar 

  217. Watkins LM, Mahoney HJ, McCulloch JK, Raushel FM (1997) Augmented hydrolysis of diisopropyl fluorophosphate in engineered mutants of phosphotriesterase. J Biol Chem 272(41):25596–25601

    Article  CAS  PubMed  Google Scholar 

  218. Chen-Goodspeed M, Sogorb MA, Wu F, Raushel FM (2001) Enhancement, relaxation, and reversal of the stereoselectivity for phosphotriesterase by rational evolution of active site residues. Biochemistry 40(5):1332–1339

    Article  CAS  PubMed  Google Scholar 

  219. Cho CM, Mulchandani A, Chen W (2002) Bacterial cell surface display of organophosphorus hydrolase for selective screening of improved hydrolysis of organophosphate nerve agents. Appl Environ Microbiol 68(4):2026–2030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Griffiths AD, Tawfik DS (2003) Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization. EMBO J 22(1):24–35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Hill CM, Li WS, Thoden JB, Holden HM, Raushel FM (2003) Enhanced degradation of chemical warfare agents through molecular engineering of the phosphotriesterase active site. J Am Chem Soc 125(30):8990–8991

    Article  CAS  PubMed  Google Scholar 

  222. Cho CM, Mulchandani A, Chen W (2004) Altering the substrate specificity of organophosphorus hydrolase for enhanced hydrolysis of chlorpyrifos. Appl Environ Microbiol 70(8):4681–4685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  223. Tsai PC, Fan Y, Kim J, Yang L, Almo SC, Gao YQ, Raushel FM (2010) Structural determinants for the stereoselective hydrolysis of chiral substrates by phosphotriesterase. Biochemistry 49(37):7988–7997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Bigley AN, Xu C, Henderson TJ, Harvey SP, Raushel FM (2013) Enzymatic neutralization of the chemical warfare agent VX: evolution of phosphotriesterase for phosphorothiolate hydrolysis. J Am Chem Soc 135(28):10426–10432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  225. Cherny I, Greisen P Jr, Ashani Y, Khare SD, Oberdorfer G, Leader H, Baker D, Tawfik DS (2013) Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries. ACS Chem Biol 8(11):2394–2403

    Article  CAS  PubMed  Google Scholar 

  226. Jackson CJ, Weir K, Herlt A, Khurana J, Sutherland TD, Horne I, Easton C, Russell RJ, Scott C, Oakeshott JG (2009) Structure-based rational design of a phosphotriesterase. Appl Environ Microbiol 75(15):5153–5156

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Naqvi T, Warden AC, French N, Sugrue E, Carr PD, Jackson CJ, Scott C (2014) A 5000-fold increase in the specificity of a bacterial phosphotriesterase for malathion through combinatorial active site mutagenesis. PLoS One 9(4):e94177

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  228. Aharoni A, Gaidukov L, Yagur S, Toker L, Silman I, Tawfik DS (2004) Directed evolution of mammalian paraoxonases PON1 and PON3 for bacterial expression and catalytic specialization. Proc Natl Acad Sci U S A 101(2):482–487

    Article  CAS  PubMed  Google Scholar 

  229. Amitai G, Gaidukov L, Adani R, Yishay S, Yacov G, Kushnir M, Teitlboim S, Lindenbaum M, Bel P, Khersonsky O, Tawfik DS, Meshulam H (2006) Enhanced stereoselective hydrolysis of toxic organophosphates by directly evolved variants of mammalian serum paraoxonase. FEBS J 273(9):1906–1919

    Article  CAS  PubMed  Google Scholar 

  230. Gupta RD, Goldsmith M, Ashani Y, Simo Y, Mullokandov G, Bar H, Ben-David M, Leader H, Margalit R, Silman I, Sussman JL, Tawfik DS (2011) Directed evolution of hydrolases for prevention of G-type nerve agent intoxication. Nat Chem Biol 7(2):120–125

    Article  CAS  PubMed  Google Scholar 

  231. Tsai PC, Bigley A, Li Y, Ghanem E, Cadieux CL, Kasten SA, Reeves TE, Cerasoli DM, Raushel FM (2010) Stereoselective hydrolysis of organophosphate nerve agents by the bacterial phosphotriesterase. Biochemistry 49(37):7978–7987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  232. Sepp A, Tawfik DS, Griffiths AD (2002) Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry. FEBS Lett 532(3):455–458

    Article  CAS  PubMed  Google Scholar 

  233. Tsai PC, Fox N, Bigley AN, Harvey SP, Barondeau DP, Raushel FM (2012) Enzymes for the homeland defense: optimizing phosphotriesterase for the hydrolysis of organophosphate nerve agents. Biochemistry 51(32):6463–6475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  234. Bigley AN, Mabanglo MF, Harvey SP, Raushel FM (2015) Variants of phosphotriesterase for the enhanced detoxification of the chemical warfare sgent VR. Biochemistry 54(35):5502–5512

    Article  CAS  PubMed  Google Scholar 

  235. Horne I, Sutherland TD, Harcourt RL, Russell RJ, Oakeshott JG (2002) Identification of an opd (organophosphate degradation) gene in an Agrobacterium isolate. Appl Environ Microbiol 68(7):3371–3376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stefan Lutz .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Lutz, S., Williams, E., Muthu, P. (2017). Engineering Therapeutic Enzymes. In: Alcalde, M. (eds) Directed Enzyme Evolution: Advances and Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-50413-1_2

Download citation

Publish with us

Policies and ethics