1.1.2 Enzyme Classification and Nomenclature and Biocatalytic Retrosynthesis

A. Liese; L. Pesci

Abstract

The enzyme nomenclature system is based on six different enzyme classes, defined by the type of chemical reaction catalyzed; hence, for a given synthetic step, it is possible to plan an enzymatic transformation (even thinking in a retrosynthetic manner) for the synthesis and/or modification of a certain compound. With this premise, the possibility of combining the methods of traditional chemical retrosynthesis with biocatalytic transformations provides an enormous potential benefit for organic chemists, including the use of modern feedstocks and “sustainable chemistry” criteria. In this chapter, enzyme nomenclature is discussed, and the related information is used as a basis for applying biocatalytic retrosynthetic analysis to several classes of organic molecules. Some key examples are provided in order to appreciate the real potential of biocatalytic retrosynthesis, especially when used in combination with more traditional chemical strategies.

Schlüsselwörter

enzyme nomenclature - reaction types - organic synthesis - retrosynthesis - green chemistry

• 1 Aelhe W, Enzymes in Industry Aelhe W. Wiley-VCH Weinheim, Germany 2007; 2

• 2 Enzyme Nomenclature: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse; available online at http://www.chem.qmul.ac.uk/iubmb/enzyme/ (accessed April 30, 2014).

• 3 Boyce S, Tipton KF. Enzyme Classification and Nomenclature. Wiley; Chichester, UK 2005

• 4 Tipton K, Boyce S. Bioinformatics 2000; 16: 34

• 5 www.brenda-enzymes.org (accessed April 22, 2014).

• 6 Liese A, Seelbach K, Buchholz A, Haberland J, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 161–163

• 7 enzymes.expasy.org (accessed April 22, 2014).

• 8 www.enzyme-database.org (accessed April 22, 2014).

• 9 Schomburg I, Chang A, Placzek S, Söhngen A, Rother M, Lang M, Munaretto C, Ulas S, Stelzer M, Grote A, Scheer M, Schomburg D. Nucleic Acids Res. 2013; 41: D764

• 10 Corey EJ, Cheng X.-M. The Logic of Chemical Synthesis Wiley Hoboken, NJ 1989; 6

• 11 Lipinsky ES. Science (Washington, D. C.) 1981; 212: 1465

• 12 Biorefineries – Industrial Processes and Products. Kamm B, Gruber PR, Kamm M. Wiley-VCH; Weinheim, Germany 2006

• 13 Vennestrøm PNR, Christensen CH, Pedersen S, Grunwaldt J, Woodley JM. ChemCatChem 2010; 2: 249

• 14 Turner NJ, OʼReilly E. Nat. Chem. Biol. 2013; 9: 285

• 15 Nath A, Atkins WM. Biochemistry 2008; 47: 157

• 16 Bornscheuer UT, Pohl M. Curr. Opin. Chem. Biol. 2001; 5: 137

• 17 Hult K, Berglund P. Trends Biotechnol. 2007; 25: 231

• 18 Winkler CK, Tasnádi G, Clay D, Hall M, Faber K. J. Biotechnol. 2012; 162: 381

• 19 Choi YJ, Lee SY. Nature (London) 2013; 502: 571

• 20 Han L, Lobo S, Reynolds KA. J. Bacteriol. 1998; 180: 4481

• 21 Dennis M, Kolattukudy PE. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 5306

• 22 Ohta H, Sugai T, Stereoselective Biocatalysis Patel RN. CRC Boca Raton, FL 2000; 467

• 23 Shanklin J, Guy JE, Mishra G, Lindqvist Y. J. Biol. Chem. 2009; 284: 18559

• 24 Rude MA, Baron TS, Brubaker S, Alibhai M, Del Cardayre SB, Schirmer A. Appl. Environ. Microbiol. 2011; 77: 1718

• 25 Kroutil W, Fischereder E, Fuchs CS, Lechner H, Mutti FG, Pressnitz D, Rajagopalan A, Sattler JH, Simon RC, Siirola E. Org. Process Res. Dev. 2013; 17: 751

• 26 Busto E, Gotor-Fernández V, Gotor V. Chem. Rev. 2011; 111: 3998

• 27 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 65

• 28 Leipold F, Hussain S, Ghislieri D, Turner NJ. ChemCatChem 2013; 5: 3505

• 29 Ghislieri D, Turner NJ. Top. Catal. 2014; 57: 284

• 30 Faber K. Biotransformations in Organic Chemistry Springer Berlin 2011; 63

• 31 Chamouleau F, Hagedorn C, May O, Gröger H. Flavour Fragrance J. 2007; 22: 169

• 32 Richter N, Neumann M, Liese A, Wohlgemuth R, Eggert T, Hummel W. ChemBioChem 2009; 10: 1888

• 33 Goldberg K, Schroer K, Lütz S, Liese A. Appl. Microbiol. Biotechnol. 2007; 76: 237

• 34 Schober M, Faber K. Trends Biotechnol. 2013; 31: 468

• 35 Borén L, Martín-Matute B, Xu Y, Córdova A, Bäckvall J.-E. Chem.–Eur. J. 2006; 12: 225

• 36 Huisman GW, Liang J, Krebber A. Curr. Opin. Chem. Biol. 2010; 14: 122

• 37 Kourist R, Bornscheuer UT. Appl. Microbiol. Biotechnol. 2011; 91: 505

• 38 Kroutil W, Mang H, Edegger K, Faber K. Adv. Synth. Catal. 2004; 346: 125

• 39 He A, Li. T, Daniels L, Fotheringham I, Rosazza JPN. Appl. Environ. Microbiol. 2004; 70: 1874

• 40 Mino T, Matsuda T, Hiramatsu D, Yamashita M. Tetrahedron Lett. 2000; 41: 1461

• 41 Archelas A, Furstoss R. Annu. Rev. Microbiol. 1997; 51: 491

• 42 Nolan LC, OʼConnor KE. Biotechnol. Lett. 2008; 30: 1879

• 43 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 68

• 44 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 70

• 45 Singh R, Sharma R, Tewari NG, Rawat DS. Chem. Biodiversity 2006; 3: 1279

• 46 Wuensch C, Glueck SM, Gross J, Koszelewski D, Schober M, Faber K. Org. Lett. 2012; 14: 1974

• 47 Mihovilovic MD, Müller B, Stanetty P. Eur. J. Org. Chem. 2002; 3711

• 48 Crich JZ, Brieva R, Marquart P, Gu R.-L, Flemming S, Sih CJ. J. Org. Chem. 1993; 58: 3252

• 49 Drauz K, Kottenhahn M, Makryaleas K, Klenk H, Bernd M. Angew. Chem. Int. Ed. Engl. 1991; 30: 712

• 50 Havir EA, Hanson KR. Biochemistry 1968; 7: 1904

• 51 Nagasawa T, Hosono H, Ohkishi H, Tani Y, Yamada H. Biochem. Biophys. Res. Commun. 1983; 111: 809

• 52 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 74

• 53 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 424

• 54 Hoh C, Villela MF, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 48, 49

• 55 Gong J, Lu Z, Li H, Shi J, Zhou Z, Xu Z. Microb. Cell Fact. 2012; 11: 142

• 56 Faber K. Biotransformations in Organic Chemistry Springer Berlin 2011; 177

• 57 Faber K. Biotransformations in Organic Chemistry Springer Berlin 2011; 238

• 58 Fesko K, Gruber-Khadjawi M. ChemCatChem 2013; 5: 1248

• 59 Fuganti C, Grasselli P, Poli G, Servi S, Zorzella A. J. Chem. Soc., Chem. Commun. 1988; 1619

• 60 Dünkelmann P, Kolter-Jung D, Nitsche A, Demir AS, Siegert P, Lingen B, Baumann M, Pohl M, Müller M. J. Am. Chem. Soc. 2002; 124: 12084

• 61 Lehwald P, Richter M, Röhr C, Liu HW, Müller M. Angew. Chem. Int. Ed. 2010; 49: 2389

• 62 Fessner W.-D, Asymmetric Organic Synthesis with Enzymes Gotor V, Alfonso I, García-Urdiales E. Wiley-VCH Weinheim, Germany 2008; 275

• 63 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 80

• 64 Dadashipour M, Asano Y. ACS Catal. 2011; 1: 1121

• 65 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 81

• 66 Millner SE, Moody TS, Maguire AR. Eur. J. Org. Chem. 2012; 3059

• 67 Peñéñory AB, Argüello JE, Puiatti M. Eur. J. Org. Chem. 2005; 114

• 68 de Gonzalo G, Torres Pazmiño DE, Ottolina G, Fraaije MW, Carrea G. Tetrahedron: Asymmetry 2005; 16: 3077

• 69 Murphy CD. J. Appl. Microbiol. 2003; 94: 539

• 70 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 83

• 71 Karich A, Kluge M, Ullrich R, Hofrichter M. AMB Express 2013; 3: 5

• 72 Shoji O, Kunimatsu T, Kawakami N, Watanabe Y. Angew. Chem. Int. Ed. 2013; 52: 6606

• 73 Gibson DT, Parales RE. Curr. Opin. Biotechnol. 2000; 11: 236

• 74 Guazzaroni M, Crestini C, Saladino R. Bioorg. Med. Chem. 2011; 20: 157

• 75 Schmitt MM, Schüler E, Braun M, Häring D, Schreier P. Tetrahedron Lett. 1998; 39: 2945

• 76 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 69

• 77 Faber K. Biotransformations in Organic Chemistry Springer Berlin 2011; 57

• 78 Turan Y, Sinan O. Pak. J. Bot. 2005; 37: 299

• 79 Tao J, Pettman A, Liese A, Industrial Biotransformations Liese A, Seelbach K, Wandrey C. Wiley-VCH Weinheim, Germany 2006; 84

• 80 Luzhetskyy A, Bechthold A. Appl. Microbiol. Biotechnol. 2008; 80: 945

• 81 Rowan AS, Hamilton CJ. Nat. Prod. Rep. 2006; 23: 412

• 82 Rauvolfová J, Weignerová L, Kuzma M, Přikrylová V, Macková M, Pišvejcová A, Křen V. J. Mol. Catal. B: Enzym. 2004; 29: 259

• 83 van Herk T, Hartog AF, van der Burg AM, Wever R. Adv. Synth. Catal. 2005; 347: 1155

• 84 Siedow JN. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1991; 42: 145

• 85 Huang F, Schwab W. BMC Biotechnol. 2011; 11: 1

• 86 Faber K. Biotransformations in Organic Chemistry Springer Berlin 2011; 200

• 87 Kobayashi S. Proc. Jpn. Acad. Ser. B 2007; 83: 215

• 88 Kadokawa J, Kobayashi S. Curr. Opin. Chem. Biol. 2010; 14: 145

• 89 Kobayashi S. Macromol. Rapid Commun. 2009; 30: 237

• 90 Gu Q.-M, Maslanka WW, Cheng HN. Polymer Prepr. (Am. Chem. Soc., Div. Polym. Chem.) 2006; 47: 234

• 91 Uyama H, Kobayashi S, Enzyme-Catalyzed Synthesis of Polymers Kobayashi S, Ritter H, Kaplan D. Springer Berlin 2006; 51

• 92 Meyer H, Eichhorn E, Hanlon S, Lütz S, Schürmann M, Wohlgemuth R, Coppolecchia R. Catal. Sci. Technol. 2013; 3: 29

• 93 Kawato Y, Chaudhary S, Kumagai N, Shibasaki M. Chem.–Eur. J. 2013; 19: 3802

• 94 Schmidt M, Böttcher D, Bornscheuer UT, Industrial Biotechnology: Sustainable Growth and Economic Success Soetaert W, Vandamme EJ. Wiley-VCH Weinheim, Germany 2010; 190

• 95 Dean SM, Greenberg WA, Wong C.-H. Adv. Synth. Catal. 2007; 349: 1308