Towards Virtual Biocatalysis

Towards Virtual Biocatalysis
Author: Anna Tomberg
Publisher:
Total Pages:
Release: 2018
Genre:
ISBN:

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"Presently, most industrial chemical production relies on catalytic processes, that represent an economical and more environmentally friendly alternative to classic stoichiometric methodologies. The use of organometallic catalysts enables many difficult chemical transformations due to the ability of transition metals to activate organic molecules. However, even catalytic amounts of metals remain a major environmental issue. The beginning of the 21st century was marked by the establishment of biocatalysis in industry as green alternative to metallo- and organometallic catalysis. Biocatalysts are fascinating bio-machines characterized by high selectivity, biodegradability and operation under mild, environmentally friendly conditions. The vast majority of biocatalysts are enzymes, proteins that have a catalytic function. One reason for the rapid progress in this field is the increasing use of computational tools in protein engineering and the ever-growing structural information available. This thesis describes a series of studies of organometallic (bio)-catalysts using several computational techniques. The goals have been to gain a deeper understanding of the range of capabilities of the (bio)-catalysts studied, and to develop new tools that can be helpful in medicinal chemistry and in biocatalysis projects.First, a review of biocatalysts and organometallic (bio)-catalysts is presented from the point of view of computational chemistry. Next, a mechanistic study of a ruthenium catalyzed coupling reaction is described: using DFT, a number of potential pathways are evaluated and a complex catalytic cycle is elucidated. In practice, such detailed investigations can only be done for a selected number of molecules and with metal complexes of limited size. While the ruthenium catalyst was modeled without truncation, using DFT on the entire active site of an enzyme is not an option. Molecular properties and descriptors that are fast to compute can replace lengthy calculations, albeit with reduced accuracy. In the study of the catalytic complex of Cytochrome P450s metabolizing enzymes described next, a truncated version of the oxo-iron heme complex is used. A detailed DFT study of an aromatic oxidation reaction catalyzed by this complex is presented and a method to predict the product drug oxidation using Frontier Molecular Orbital theory is outlined. The use of local reactivity descriptors was then probed as a way to further increase the accuracy of sites of oxidation prediction. However, reactivity of substrates is not the only property that influences the selectivity of oxidation. The structure of the active site plays an important role as well. With smaller systems such as the ruthenium complex, several conformations can be generated and examined. This approach is inappropriate for larger systems such as enzymes. To study how the structure of the catalytic site impacts the selectivity of Cytochrome P450s, a method for virtual mutagenesis was developed. Structural changes induced by mutations were modeled using Normal Mode Analysis and a rotamer library toolkit (previously reported). The potential of the programs developed for virtual biocatalysis design was demonstrated using a case study on Cytochrome P450s metabolic project." --

Biocatalysis

Biocatalysis
Author: W.-D. Fessner
Publisher: Springer Science & Business Media
Total Pages: 273
Release: 2003-09-05
Genre: Science
ISBN: 3540681167

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Here, leading contributors from the forefront of this exciting technology present authoritative and timely reviews on the state of the art of biocatalysis. They cover the whole spectrum from the discovery of novel enzymes - by modern screening, evolutionary or immunological approaches - through immobilization techniques for technical processes, to their use in the asymmetric synthesis of important target compounds.

Asymmetric and Selective Biocatalysis

Asymmetric and Selective Biocatalysis
Author: Jose M. Palomo
Publisher: MDPI
Total Pages: 154
Release: 2019-04-12
Genre: Science
ISBN: 3038978469

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This Issue contains one communication, six articles, and two reviews. The communication from Paola Vitale et al. represents a work where whole cells were used as biocatalysts for the reduction of optically active chloroalkyl arylketones followed by a chemical cyclization to give the desired heterocycles. Among the various whole cells screened (baker’s yeast, Kluyveromyces marxianus CBS 6556, Saccharomyces cerevisiae CBS 7336, Lactobacillus reuteri DSM 20016), baker’s yeast provided the best yields and the highest enantiomeric ratios (95:5) in the bioreduction of the above ketones. In this respect, valuable chiral non-racemic functionalized oxygen-containing heterocycles (e.g., (S)-styrene oxide, (S)-2-phenyloxetane, (S)-2-phenyltetrahydrofuran), amenable to be further elaborated on, can be smoothly and successfully generated from their prochiral precursors. Studies about pure biocatalysts with mechanistical studies, application in different reactions, and new immobilization methods for improving their stability were reported in five different articles. The article by Su-Yan Wang et al. describes the cloning, expression, purification, and characterization of an N-acetylglucosamine 2-epimerase from Pedobacter heparinus (PhGn2E). For this, several N-acylated glucosamine derivatives were chemically synthesized and used to test the substrate specificity of the enzyme. The mechanism of the enzyme was studied by hydrogen/deuterium NMR. The study at the anomeric hydroxyl group and C-2 position of the substrate in the reaction mixture confirmed the epimerization reaction via ring-opening/enolate formation. Site-directed mutagenesis was also used to confirm the proposed mechanism of this interesting enzyme. The article by Forest H. Andrews et al. studies two enzymes, benzoylformate decarboxylase (BFDC) and pyruvate decarboxylase (PDC), which catalyze the non-oxidative decarboxylation of 2-keto acids with different specificity. BFDC from Pseudomonas putida exhibited very limited activity with pyruvate, whereas the PDCs from S. cerevisiae or from Zymomonas mobilis showed virtually no activity with benzoylformate (phenylglyoxylate). After studies using saturation mutagenesis, the BFDC T377L/A460Y variant was obtained, with 10,000-fold increase in pyruvate/benzoylformate. The change was attributed to an improvement in the Km value for pyruvate and a decrease in the kcat value for benzoylformate. The characterization of the new catalyst was performed, providing context for the observed changes in the specificity. The article by Xin Wang et al. compares two types of biocatalysts to produce D-lysine L-lysine in a cascade process catalyzed by two enzymes: racemase from microorganisms that racemize L-lysine to give D,L-lysine and decarboxylase that can be in cells, permeabilized cells, and the isolated enzyme. The comparison between the different forms demonstrated that the isolated enzyme showed the higher decarboxylase activity. Under optimal conditions, 750.7 mmol/L D-lysine was finally obtained from 1710 mmol/L L-lysine after 1 h of racemization reaction and 0.5 h of decarboxylation reaction. D-lysine yield could reach 48.8% with enantiomeric excess (ee) of 99%. In the article by Rivero and Palomo, lipase from Candida rugosa (CRL) was highly stabilized at alkaline pH in the presence of PEG, which permitted its immobilization for the first time by multipoint covalent attachment on different aldehyde-activated matrices. Different covalent immobilized preparation of the enzyme was successfully obtained. The thermal and solvent stability was highly increased by this treatment, and the novel catalysts showed high regioselectivity in the deprotection of per-O-acetylated nucleosides. The article by Robson Carlos Alnoch et al. describes the protocol and use of a new generation of tailor-made bifunctional supports activated with alkyl groups that allow the immobilization of proteins through the most hydrophobic region of the protein surface and aldehyde groups that allows the covalent immobilization of the previously adsorbed proteins. These supports were especially used in the case of lipase immobilization. The immobilization of a new metagenomic lipase (LipC12) yielded a biocatalyst 3.5-fold more active and 5000-fold more stable than the soluble enzyme. The PEGylated immobilized lipase showed high regioselectivity, producing high yields of the C-3 monodeacetylated product at pH 5.0 and 4 °C. Hybrid catalysts composed of an enzyme and metallic complex are also treated in this Special Issue. The article by Christian Herrero et al. describes the development of the Mn(TpCPP)-Xln10A artificial metalloenzyme, obtained by non-covalent insertion of Mn(III)-meso-tetrakis(p-carboxyphenyl)porphyrin [Mn(TpCPP), 1-Mn] into xylanase 10A from Streptomyces lividans (Xln10A). The complex was found able to catalyze the selective photo-induced oxidation of organic substrates in the presence of [RuII(bpy)3]2+ as a photosensitizer and [CoIII(NH3)5Cl]2+ as a sacrificial electron acceptor, using water as oxygen atom source. The two published reviews describe different subjects with interest in the fields of biocatalysis and mix metallic-biocatalysis, respectively. The review by Anika Scholtissek et al. describes the state-of-the-art regarding ene-reductases from the old yellow enzyme family (OYEs) to catalyze the asymmetric hydrogenation of activated alkenes to produce chiral products with industrial interest. The dependence of OYEs on pyridine nucleotide coenzyme can be avoided by using nicotinamide coenzyme mimetics. In the review, three main classes of OYEs are described and characterized. The review by Yajie Wang and Huimin Zhao highlights some of the recent examples in the past three years that combine transition metal catalysis with enzymatic catalysis. With recent advances in protein engineering, catalyst synthesis, artificial metalloenzymes, and supramolecular assembly, there is great potential to develop more sophisticated tandem chemoenzymatic processes for the synthesis of structurally complex chemicals. In conclusion, these nine publications give an overview of the possibilities of different catalysts, both traditional biocatalysts and hybrids with metals or organometallic complexes to be used in different processes—particularly in synthetic reactions—under very mild reaction conditions.

Biocatalysis

Biocatalysis
Author: Andreas S. Bommarius
Publisher: John Wiley & Sons
Total Pages: 634
Release: 2007-02-27
Genre: Science
ISBN: 352760605X

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The whole range of biocatalysis, from a firm grounding in theoretical concepts to in-depth coverage of practical applications and future perspectives. The book not only covers reactions, products and processes with and from biological catalysts, but also the process of designing and improving such biocatalysts. One unique feature is that the fields of chemistry, biology and bioengineering receive equal attention, thus addressing practitioners and students from all three areas.

Modern Biocatalysis

Modern Biocatalysis
Author: Gavin Williams
Publisher: Royal Society of Chemistry
Total Pages: 594
Release: 2018-05-31
Genre: Science
ISBN: 1788014537

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The synergy between synthetic biology and biocatalysis is emerging as an important trend for future sustainable processes. This book reviews all modern and novel techniques successfully implemented in biocatalysis, in an effort to provide better performing enzymatic systems and novel biosynthetic routes to (non-)natural products. This includes the use of molecular techniques in protein design and engineering, construction of artificial metabolic pathways, and application of computational methods for enzyme discovery and design. Stress is placed on current ‘hot’ topics in biocatalysis, where recent advances in research are defining new grounds in enzyme-catalyzed processes. With contributions from leading academics around the world, this book makes a ground-breaking contribution to this progressive field and is essential reading for graduates and researchers investigating (bio)catalysis, enzyme engineering, chemical biology, and synthetic biology.

Modern Biocatalysis

Modern Biocatalysis
Author: Wolf-Dieter Fessner
Publisher: John Wiley & Sons
Total Pages: 406
Release: 2009-02-09
Genre: Science
ISBN: 9783527320714

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Das Gesamtgebiet der Biokatalyse mit allen seinen Facetten -- Mikrobiologie, Enzymologie, Molekularbiologie, Strukturbiologie, organische Chemie -- wird in diesem interdisziplinär angelegten Werk beleuchtet; insbesondere geht es um enzymatische Katalysen und Ganzzell-Katalysen. Ein Schwerpunkt liegt dabei auf der Entwicklung hochselektiver, umweltfreundlicher Prozesse zur Synthese wichtiger Verbindungsklassen.

Biocatalysis

Biocatalysis
Author: Gonzalo de Gonzalo
Publisher: Royal Society of Chemistry
Total Pages: 532
Release: 2017-11-02
Genre: Science
ISBN: 1788012461

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Implementing biocatalytic strategies in an industrial setting at a commercial scale is a challenging task, necessitating a balance between industrial need against economic viability. With invited contributions from small and large-scale chemical and pharmaceutical companies, this book bridges the gap between academia and industry. Contributors discuss current processes, types of biocatalysts and improvements, industrial motivation and key aspects to economically succeed. With its focus on industry related issues, this book will be a useful tool for future research by both practitioners and academics.

Enzyme Biocatalysis

Enzyme Biocatalysis
Author: Andrés Illanes
Publisher: Springer Science & Business Media
Total Pages: 398
Release: 2008-06-19
Genre: Technology & Engineering
ISBN: 1402083610

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This book was written with the purpose of providing a sound basis for the design of enzymatic reactions based on kinetic principles, but also to give an updated vision of the potentials and limitations of biocatalysis, especially with respect to recent app- cations in processes of organic synthesis. The ?rst ?ve chapters are structured in the form of a textbook, going from the basic principles of enzyme structure and fu- tion to reactor design for homogeneous systems with soluble enzymes and hete- geneous systems with immobilized enzymes. The last chapter of the book is divided into six sections that represent illustrative case studies of biocatalytic processes of industrial relevance or potential, written by experts in the respective ?elds. We sincerely hope that this book will represent an element in the toolbox of gr- uate students in applied biology and chemical and biochemical engineering and also of undergraduate students with formal training in organic chemistry, biochemistry, thermodynamics and chemical reaction kinetics. Beyond that, the book pretends also to illustrate the potential of biocatalytic processes with case studies in the ?eld of organic synthesis, which we hope will be of interest for the academia and prof- sionals involved in R&D&I. If some of our young readers are encouraged to engage or persevere in their work in biocatalysis this will certainly be our more precious reward.

Applied Biocatalysis

Applied Biocatalysis
Author: John Whittall
Publisher: John Wiley & Sons
Total Pages: 560
Release: 2020-08-21
Genre: Science
ISBN: 111948703X

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Provides clear and comprehensive coverage of recently developed applied biocatalysis for synthetic organic chemists with an emphasis to promote green chemistry in pharmaceutical and process chemistry This book aims to make biocatalysis more accessible to both academic and industrial synthetic organic chemists. It focuses on current topics within the applied industrial biocatalysis field and includes short but detailed experimental methods on timely novel biocatalytic transformations using new enzymes or new methodologies using known enzymes. The book also features reactions that are “expanding and making the enzyme toolbox available to chemists”—providing readers with comprehensive methodology and detailed key sourcing information of a wide range of enzymes. Chapters in Applied Biocatalysis: The Chemist’s Enzyme Toolkit are organized by reaction type and feature a short introductory section describing the current state of the art for each example. Much of the book focuses on processes for which the enzymes are readily available so that organic chemists can synthesize appropriate quantities of chemicals with available materials in a standard chemical laboratory. Advanced methods are included to present examples of new enzymes that might encourage collaboration with suppliers or academic groups and that will educate chemists of rapidly expanding future possibilities. Focuses on current topics within the applied industrial biocatalysis field Offers experimental methods on novel biocatalytic transformations using new enzymes or new methodology using known enzymes Covers the hot topics of enzyme and chemoenzymatic cascades and biocatalysis in flow Edited by noted experts from both academia and industry with years of experience in the field of biocatalysis—particularly, the industrial applications of enzymes Written for synthetic organic chemists working in all industries but especially the pharmaceutical industry and for those in academia with an eye for biocatalysis, Applied Biocatalysis: The Chemist’s Enzyme Toolkit will also benefit academic groups in chemistry and related sciences that are using enzymes for synthetic purposes, as well as those working in the area of enzymology and molecular biology.

Biocatalysis for Practitioners

Biocatalysis for Practitioners
Author: Gonzalo de Gonzalo
Publisher: John Wiley & Sons
Total Pages: 54
Release: 2021-04-13
Genre: Science
ISBN: 3527824456

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This reference book originates from the interdisciplinary research cooperation between academia and industry. In three distinct parts, latest results from basic research on stable enzymes are explained and brought into context with possible industrial applications. Downstream processing technology as well as biocatalytic and biotechnological production processes from global players display the enormous potential of biocatalysts. Application of "extreme" reaction conditions (i.e. unconventional, such as high temperature, pressure, and pH value) - biocatalysts are normally used within a well defined process window - leads to novel synthetic effects. Both novel enzyme systems and the synthetic routes in which they can be applied are made accessible to the reader. In addition, the complementary innovative process technology under unconventional conditions is highlighted by latest examples from biotech industry.