Enzymes in Organic Chemistry

Course manual 2024/2025

Course content

The course "Enzymes in Organic Chemistry" provides a detailed overview of the enzymatic methods currently applied in organic chemical synthesis, both at laboratory and industrial scales. It also offers fundamental knowledge on how enzymes can be engineered to meet the requirements for their use in chemical synthesis.In detail, fundamental concepts of enzyme catalysis, such as enzyme classification and general enzymatic mechanisms, are reviewed and expanded at the beginning of the course. Next, the main classes of enzymes employed in organic synthesis—such as hydrolases, oxidoreductases, transferases, and enzymes for C-C bond formation—are discussed. The related specific synthetic strategies (e.g., kinetic and dynamic kinetic resolution, deracemization, asymmetric synthesis) are introduced progressively and critically analyzed. Furthermore, another aim of the course is to bridge knowledge and concepts between biocatalysis, organic synthesis, and chemo-catalysis within the broad field of synthetic organic chemistry. These concepts are further expanded by introducing biocatalytic retrosynthesis, which integrates enzyme-catalyzed reactions into traditional chemical retrosynthetic analysis. This is exemplified in a problem session on biocatalytic retrosynthesis, where these concepts are applied. Ad-hoc lectures on artificial enzymes also demonstrate how biocatalysis can be merged with chemocatalysis, in certain cases, to catalyze reactions not known to occur in nature. Finally, the course provides fundamental knowledge on strategies for enzyme engineering based on directed evolution and rational design.

Study Goals

One of the main goals of the M.Sc. education in Molecular Sciences is the development of knowledge and understanding of the reactions and reactivity of organic compounds. In this context, nature catalyzes a myriad of chemical reactions for the synthesis of organic compounds that possess varied levels of structural complexity. Broadly, the aim of the course 'Enzymes in Organic Chemistry' is to provide a critical overview of synthetic strategies that utilize the available classes of biocatalysts and their combination with complementary methodologies.

Objectives

• To classify enzyme families based on type of reaction, substrate converted, cosubstrate and cofactor involved, eventually formed coproduct.
• To explain and sketch the mechanism of selected enzymatic reactions.
• To describe and apply the fundamental definitions in enzyme catalysis and asymmetric synthesis (e.g. activity units, selectivity, turnover, enzymatic kinetic constants, enantiomeric/diastereomeric excess).
• To distinguish among different biocatalytic strategies in organic synthesis and provide examples on those.
• To memorise, summarize, apply, compare and combine the different classes of enzymes in organic synthesis.
• To sketch biocatalytic reactions and pathways for the synthesis of important family of compounds.
• To conceive a retrosynthetic plan for the synthesis of relatively simple organic molecules in which, at least, an enzymatic step is incorporated (i.e., affording an advantage such as shortening the length of the synthesis and/or increasing selectivity and/or reducing generation of waste).
• To assess pros and cons when comparing a biocatalytic reactions with a chemocatalytic or non-catalyzed reaction for a given chemical transformation.
• To illustrate principles and methods in enzyme engineering and analyse pros and cons for each method.
• To describe the basic principles behind tandem and cascade reactions and relate them to major biosynthesis routes.
• To classify multi-step biocatalytic processes (sequential, concurrent, parallel, orthogonal, etc.) and apply them through examples in organic synthesis.
• To define the fundamental terminology in molecular biology and summarize the steps for the preparation of an enzyme in the lab.
• To illustrate principles and methods for the generation of artificial enzymes and related them with concepts of organometallic- and organo-catalysis.

Teaching methods

• Lecture
• Self-study
• problem solving sessions

Learning activities

Attendance

This programme does not have requirements concerning attendance (TER part B).

Assessment

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• dr. Francesco Mutti