Biocatalysis: A Status Report.

This review describes the status of the fields of biocatalysts and enzymes, as well as existing drawbacks, and recent advances in the areas deemed to represent drawbacks. Although biocatalysts are often highly active and extremely selective, there are still drawbacks associated with biocatalysis as a generally applicable technique: the lack of designability of biocatalysts; their limits of stability; and the insufficient number of well-characterized, ready-to-use biocatalysts. There has been significant progress on the following fronts: (a) novel protein engineering tools, both experimental and computational, have significantly enhanced the toolbox for biocatalyst development. (b) The deactivation of biocatalysts under various stresses can be described quantitatively via rational models. There are several cases of spectacular leaps of stabilization after accumulating all stabilizing mutations found in earlier rounds. The concept that stabilization against one type of stress commonly also stabilizes against other types of stress is now experimentally considerably better founded than a few years ago.

[1]  D. Tirrell,et al.  Noncanonical amino acids in the interrogation of cellular protein synthesis. , 2011, Accounts of chemical research.

[2]  Paul Dupree,et al.  An evolutionary route to xylanase process fitness , 2004, Protein science : a publication of the Protein Society.

[3]  Nicholas J Turner,et al.  Directed evolution drives the next generation of biocatalysts. , 2009, Nature chemical biology.

[4]  M. Kula,et al.  Stabilization of NAD-dependent formate dehydrogenase from Candida boidinii by site-directed mutagenesis of cysteine residues. , 2000, European journal of biochemistry.

[5]  S. Steinbacher,et al.  Sequence statistics reliably predict stabilizing mutations in a protein domain. , 1994, Journal of molecular biology.

[6]  Eric A. Althoff,et al.  Kemp elimination catalysts by computational enzyme design , 2008, Nature.

[7]  Manfred T Reetz,et al.  Laboratory evolution of enantiocomplementary Candida antarctica lipase B mutants with broad substrate scope. , 2013, Journal of the American Chemical Society.

[8]  Paul N. Devine,et al.  Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture , 2010, Science.

[9]  F. Hollfelder,et al.  One-Pot Deracemization of sec-Alcohols: Enantioconvergent Enzymatic Hydrolysis of Alkyl Sulfates Using Stereocomplementary Sulfatases** , 2013, Angewandte Chemie.

[10]  Martin Lehmann,et al.  The consensus concept for thermostability engineering of proteins: further proof of concept. , 2002, Protein engineering.

[11]  A. Fersht Structure and mechanism in protein science , 1998 .

[12]  Nikolaus G. Turrini,et al.  Nitrile as Activating Group in the Asymmetric Bioreduction of β-Cyanoacrylic Acids Catalyzed by Ene-Reductases , 2014, Advanced synthesis & catalysis.

[13]  D. Weuster‐Botz,et al.  Enantiocomplementary inverting sec-alkylsulfatase activity in cyano- and thio-bacteria Synechococcus and Paracoccus spp.: selectivity enhancement by medium engineering , 2009 .

[14]  F. Arnold,et al.  Cytochrome P450-Catalyzed Insertion of Carbenoids into N-H Bonds. , 2014, Chemical science.

[15]  Janna K Blum,et al.  Improved thermostability of AEH by combining B-FIT analysis and structure-guided consensus method. , 2012, Journal of biotechnology.

[16]  Manfred T Reetz,et al.  Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions. , 2011, Angewandte Chemie.

[17]  Manfred T Reetz,et al.  Creation of an amino acid network of structurally coupled residues in the directed evolution of a thermostable enzyme. , 2009, Angewandte Chemie.

[18]  Andreas S Bommarius,et al.  Utilizing Simple Biochemical Measurements to Predict Lifetime Output of Biocatalysts in Continuous Isothermal Processes. , 2010, Chemical engineering science.

[19]  Hein J. Wijma,et al.  Computationally designed libraries for rapid enzyme stabilization , 2014, Protein engineering, design & selection : PEDS.

[20]  Manfred T Reetz,et al.  Addressing the Numbers Problem in Directed Evolution , 2008, Chembiochem : a European journal of chemical biology.

[21]  N. Oppenheimer,et al.  Structure and mechanism , 1989 .

[22]  Wolfgang Kroutil,et al.  Deracemization By Simultaneous Bio-oxidative Kinetic Resolution and Stereoinversion , 2014, Angewandte Chemie.

[23]  A. Böck,et al.  Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Frances H. Arnold,et al.  A Serine-Substituted P450 Catalyzes Highly Efficient Carbene Transfer to Olefins In Vivo , 2013, Nature chemical biology.

[25]  Jijun Hao,et al.  A thermostable variant of fructose bisphosphate aldolase constructed by directed evolution also shows increased stability in organic solvents. , 2004, Protein engineering, design & selection : PEDS.

[26]  D. Cowan,et al.  Correlation between microbial protein thermostability and resistance to denaturation in aqueous-organic solvent 2-phase systems , 1989 .

[27]  Henry Eyring,et al.  Conformation Changes of Proteins , 1954 .

[28]  G. Whitesides,et al.  Kinetic resolution of unnatural and rarely occurring amino acids: enantioselective hydrolysis of N-acyl amino acids catalyzed by acylase I , 1989 .

[29]  Yosephine Gumulya,et al.  Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method. , 2010, Chemical communications.

[30]  J. Raftery,et al.  Enantioselective biocatalytic oxidative desymmetrization of substituted pyrrolidines. , 2010, Angewandte Chemie.

[31]  P. Macheroux,et al.  The Substrate Spectrum of the Inverting sec-Alkylsulfatase Pisa1 , 2012 .

[32]  D. R. Palmer,et al.  The lesser "burden borne" by o-succinylbenzoate synthase: an "easy" reaction involving a carboxylate carbon acid. , 2001, Journal of the American Chemical Society.

[33]  Nicholas J Turner,et al.  A Regio- and Stereoselective ω-Transaminase/Monoamine Oxidase Cascade for the Synthesis of Chiral 2,5-Disubstituted Pyrrolidines , 2014, Angewandte Chemie.

[34]  N. Scrutton,et al.  Biocatalysis with Thermostable Enzymes: Structure and Properties of a Thermophilic ‘ene’‐Reductase related to Old Yellow Enzyme , 2010, Chembiochem : a European journal of chemical biology.

[35]  K. Gruber,et al.  Catalytic and Structural Role of a Conserved Active Site Histidine in Berberine Bridge Enzyme , 2012, Biochemistry.

[36]  Frances H Arnold,et al.  Expanding P450 catalytic reaction space through evolution and engineering. , 2014, Current opinion in chemical biology.

[37]  David Baker,et al.  Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59 , 2012, Proceedings of the National Academy of Sciences.

[38]  David Baker,et al.  Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. , 2010, Journal of molecular biology.

[39]  N. Turner,et al.  A highly efficient synthesis of telaprevir by strategic use of biocatalysis and multicomponent reactions. , 2010, Chemical communications.

[40]  E. Bayer,et al.  Approaches for improving thermostability characteristics in cellulases. , 2012, Methods in enzymology.

[41]  Philip A. Romero,et al.  Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. , 2010, Protein engineering, design & selection : PEDS.

[42]  Andreas Vogel,et al.  Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test. , 2005, Angewandte Chemie.

[43]  Frances H Arnold,et al.  SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability* , 2009, The Journal of Biological Chemistry.

[44]  A. Karau,et al.  Deactivation of Formate Dehydrogenase (FDH) in Solution and at Gas‐Liquid Interfaces , 2005, Biotechnology progress.

[45]  S. M. Glueck,et al.  Enzymatic Aerobic Alkene Cleavage Catalyzed by a Mn3+‐Dependent Proteinase A Homologue , 2013, Chembiochem : a European journal of chemical biology.

[46]  M. Reetz,et al.  Biocatalysis in organic chemistry and biotechnology: past, present, and future. , 2013, Journal of the American Chemical Society.

[47]  P. Harrison,et al.  The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the ‘termination’ codon, TGA. , 1986, The EMBO journal.

[48]  John D. Hayler,et al.  Key green chemistry research areas—a perspective from pharmaceutical manufacturers , 2007 .

[49]  Joseph A. Krzycki,et al.  Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA , 2002, Science.

[50]  Joerg H. Schrittwieser,et al.  Biocatalytic enantioselective oxidative C-C coupling by aerobic C-H activation. , 2011, Angewandte Chemie.

[51]  J. M. Patel Biocatalytic synthesis of atorvastatin intermediates , 2009 .

[52]  Uwe T Bornscheuer,et al.  Protein engineering from "scratch" is maturing. , 2014, Angewandte Chemie.

[53]  M. V. Filho,et al.  Chemoenzymatic synthesis of the chiral side-chain of statins: application of an alcohol dehydrogenase catalysed ketone reduction on a large scale , 2008, Bioprocess and biosystems engineering.

[54]  Junhua Tao,et al.  Biocatalysis in development of green pharmaceutical processes. , 2009, Current opinion in chemical biology.

[55]  C. Wandrey,et al.  Highly Regio- and Enantioselective Reduction of 3,5-Dioxocarboxylates. , 2000, Angewandte Chemie.

[56]  S. M. Glueck,et al.  Oxidative enzymatic alkene cleavage: indications for a nonclassical enzyme mechanism. , 2009, Journal of the American Chemical Society.

[57]  M. Lehmann,et al.  The consensus concept for thermostability engineering of proteins. , 2000, Biochimica et biophysica acta.

[58]  Junhua Tao,et al.  Development of a Chemoenzymatic Manufacturing Process for Pregabalin , 2008 .

[59]  P. Schultz,et al.  Genetic incorporation of multiple unnatural amino acids into proteins in mammalian cells. , 2013, Angewandte Chemie.

[60]  C. James,et al.  A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase , 2002, Science.

[61]  Christopher A. Voigt,et al.  Protein building blocks preserved by recombination , 2002, Nature Structural Biology.

[62]  A. Wells,et al.  Enantioselective oxidation of O-methyl-N-hydroxylamines using monoamine oxidase N as catalyst. , 2007, Chemical communications.

[63]  Thomas R Ward,et al.  Artificial metalloenzymes for olefin metathesis based on the biotin-(strept)avidin technology. , 2011, Chemical communications.

[64]  John C Whitman,et al.  Improving catalytic function by ProSAR-driven enzyme evolution , 2007, Nature Biotechnology.

[65]  P. Macheroux,et al.  A Stereoselective Inverting sec-Alkylsulfatase for the Deracemization of sec-Alcohols , 2011, Organic letters.

[66]  L. Nadeau,et al.  Characterization of hydroxylaminobenzene mutase from pNBZ139 cloned from Pseudomonas pseudoalcaligenes JS45. A highly associated SDS-stable enzyme catalyzing an intramolecular transfer of hydroxy groups. , 2000, European journal of biochemistry.

[67]  K. Katayama,et al.  Total Synthesis of (−)-Solanapyrone A via Enzymatic Diels−Alder Reaction of Prosolanapyrone , 1998 .

[68]  J. Chaparro-Riggers,et al.  Thermostable variants constructed via the structure-guided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media. , 2008, Protein engineering, design & selection : PEDS.

[69]  Sheng Hu,et al.  Altering the regioselectivity of cytochrome P450 BM-3 by saturation mutagenesis for the biosynthesis of indirubin , 2010 .

[70]  Andreas S Bommarius,et al.  Development of an amine dehydrogenase for synthesis of chiral amines. , 2012, Angewandte Chemie.

[71]  Nicholas J. Turner,et al.  Engineering an enantioselective amine oxidase for the synthesis of pharmaceutical building blocks and alkaloid natural products. , 2013, Journal of the American Chemical Society.

[72]  W. Hummel,et al.  Biocatalytic reduction of beta,delta-diketo esters: a highly stereoselective approach to all four stereoisomers of a chlorinated beta,delta-dihydroxy hexanoate. , 2001, Chemistry.

[73]  Ramesh N. Patel,et al.  Preparation of an Amino Acid Intermediate for the Dipeptidyl Peptidase IV Inhibitor, Saxagliptin, using a Modified Phenylalanine Dehydrogenase , 2007 .

[74]  A. Bommarius,et al.  The Evolution of an Amine Dehydrogenase Biocatalyst for the Asymmetric Production of Chiral Amines , 2013 .

[75]  Richard J Fox,et al.  Catalytic effectiveness, a measure of enzyme proficiency for industrial applications. , 2009, Trends in biotechnology.

[76]  Joerg H. Schrittwieser,et al.  Biocatalytic Oxidative CC Bond Formation Catalysed by the Berberine Bridge Enzyme: Optimal Reaction Conditions , 2011 .

[77]  Robert Eisenthal,et al.  Catalytic efficiency and kcat/KM: a useful comparator? , 2007, Trends in biotechnology.

[78]  Thomas R Ward,et al.  Recent achievments in the design and engineering of artificial metalloenzymes. , 2014, Current opinion in chemical biology.

[79]  Manfred T Reetz,et al.  Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes , 2007, Nature Protocols.

[80]  E. Ceccarelli,et al.  Efficiency function for comparing catalytic competence. , 2008, Trends in biotechnology.

[81]  Frances H Arnold,et al.  A family of thermostable fungal cellulases created by structure-guided recombination , 2009, Proceedings of the National Academy of Sciences.

[82]  F. Arnold,et al.  Structural, Functional, and Spectroscopic Characterization of the Substrate Scope of the Novel Nitrating Cytochrome P450 TxtE , 2014, Chembiochem : a European journal of chemical biology.

[83]  Vijay Kumar Gupta,et al.  Improved stabilization of microencapsulated Cathepsin B in harsh conditions , 2007 .

[84]  E. Notomista,et al.  Molecular Determinants of the Regioselectivity of Toluene/o-Xylene , 2008 .

[85]  J. Blanchard,et al.  Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity. , 2000, Biochemistry.

[86]  Thomas R Ward,et al.  Merging the best of two worlds: artificial metalloenzymes for enantioselective catalysis. , 2011, Chemical communications.

[87]  R. Wolfenden,et al.  A proficient enzyme. , 1995, Science.

[88]  Frances H Arnold,et al.  Improved cyclopropanation activity of histidine-ligated cytochrome P450 enables the enantioselective formal synthesis of levomilnacipran. , 2014, Angewandte Chemie.

[89]  Frances H Arnold,et al.  Enantioselective intramolecular C-H amination catalyzed by engineered cytochrome P450 enzymes in vitro and in vivo. , 2013, Angewandte Chemie.

[90]  Michael Müller,et al.  Chemoenzymatic synthesis of building blocks for statin side chains. , 2005, Angewandte Chemie.

[91]  C. Wandrey,et al.  Some New Developments in Reductive Amtnation with Cofactor Regeneration , 1994 .

[92]  S. Harayama,et al.  Significantly enhanced stability of glucose dehydrogenase by directed evolution , 2003, Applied Microbiology and Biotechnology.

[93]  D. Cowan,et al.  Thermophilic proteins: stability and function in aqueous and organic solvents. , 1997, Comparative biochemistry and physiology. Part A, Physiology.

[94]  Donald Hilvert,et al.  Precision is essential for efficient catalysis in an evolved Kemp eliminase , 2013, Nature.

[95]  M. Reetz,et al.  Enzyme promiscuity: first protein-catalyzed Morita-Baylis-Hillman reaction , 2007 .

[96]  G. Huisman,et al.  Engineering the third wave of biocatalysis , 2012, Nature.

[97]  R. Wolfenden,et al.  The depth of chemical time and the power of enzymes as catalysts. , 2001, Accounts of chemical research.

[98]  Frances H. Arnold,et al.  Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes , 2013, Science.

[99]  Manfred T Reetz,et al.  Directed evolution of enantioselective enzymes: iterative cycles of CASTing for probing protein-sequence space. , 2006, Angewandte Chemie.

[100]  Nicholas J Turner,et al.  The structure of monoamine oxidase from Aspergillus niger provides a molecular context for improvements in activity obtained by directed evolution. , 2008, Journal of molecular biology.

[101]  A. Bommarius,et al.  Enantioenriched compounds via enzyme-catalyzed redox reactions. , 2011, Chemical reviews.

[102]  K. Faber,et al.  Chemoenzymatic Asymmetric Synthesis of Pregabalin Precursors via Asymmetric Bioreduction of β-Cyanoacrylate Esters Using Ene-Reductases , 2013, The Journal of organic chemistry.

[103]  S. M. Glueck,et al.  Biocatalytic Cleavage of Alkenes with O2 and Trametes hirsuta G FCC 047 , 2008 .

[104]  Frances H Arnold,et al.  Library analysis of SCHEMA‐guided protein recombination , 2003, Protein science : a publication of the Protein Society.

[105]  L. Kay,et al.  Bringing dynamic molecular machines into focus by methyl-TROSY NMR. , 2014, Annual review of biochemistry.