Volume 50 Number 14 21 July 2021 Pages 7883–8346 Chem Soc Rev Chemical Society Reviews rsc.li/chem-soc-rev ISSN 0306-0012 REVIEW ARTICLE Uwe T. Bornscheuer et al . Recent trends in biocatalysis Chem Soc Rev View Article Online REVIEW ARTICLE View Journal | View Issue Recent trends in biocatalysis Cite this: Chem. Soc. Rev., 2021, Dong Yi, † Thomas Bayer, † Christoffel P. S. Badenhorst, † Shuke Wu, † 50, 8003 Mark Doerr, † Matthias Ho¨hne † and Uwe T. Bornscheuer * Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the Received 19th December 2020 discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually comple- DOI: 10.1039/d0cs01575j ments the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent rsc.li/chem-soc-rev manufacturing and enzymatic total synthesis. Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Introduction a completely new research field: biocatalysis.1 Over the next hundred years, this research field had developed rapidly and More than a century ago, Rosenthaler synthesised (R)-mandelo- experienced three distinct waves,2 advancing from the use of nitrile from benzaldehyde and hydrogen cyanide using a plant crude extract to purified enzymes and then to recombinant extract containing a hydroxynitrile lyase and opened the door to enzyme systems. The screening of biocatalysts had evolved from natural source extraction to gene mining with bioinfor- This article is licensed under a matic methods. Finally, sequence—structure—function analy- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, sis benefited from the developments in structural biology. University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany. E-mail: [email protected] The engineering of biocatalysts had shifted from modifying Open Access Article. Published on 18 June 2021. Downloaded 10/9/2021 12:48:46 PM. † Equal contribution. reaction conditions to suit enzymatic properties to directed Dong Yi studied chemistry sup- Thomas Bayer graduated in the ported by the Deutscher Akade- Molecular Biology programme mischer Austauschdienst (DAAD) from the University of Vienna with a doctoral scholarship at the and received his PhD in (Bio)- TU Darmstadt (Germany) and organic Chemistry at the TU obtained his PhD (summa cum Wien (Austria) before joining the laude) under supervision of Prof. Bornscheuer group as a post- Wolf-Dieter Fessner in 2012. He doctoral fellow. Thomas Bayer worked as Postdoctoral Teaching received the Erwin Schro¨dinger Fellow at the East China Uni- fellowship by The Austrian versity of Science and Tech- Science Fund (FWF), which nology (China) from 2013 and included scientific stays at the Dong Yi was involved in establishing a Thomas Bayer University of Greifswald (Germany) pharmaceutical company. In 2018, and the Albert Einstein College of he joined the Bornscheuer group at the University of Greifswald Medicine in New York City (USA) in 2019–2020. Since 2021, he works (Germany) as a postdoc and worked within the EU funded project at the Institute of Molecular Biotechnology at the TU Graz (Austria). ‘‘SynBio4Flav’’. He currently works as the Head of Systems Biosynthesis in the Shanghai Institute of Pharmaceutical Industry (China). This journal is © The Royal Society of Chemistry 2021 Chem. Soc. Rev., 2021, 50, 8003–8049 | 8003 View Article Online Review Article Chem Soc Rev evolution of enzymes to adapt to reaction conditions and into a biocatalytic network, in which the upper edges and nodes molecular structures of substrates.2 These technological revo- are connected in series to form multi-step enzymatic cascades. lutions all profited from the development and integration of These cascades made the biosynthesis of chemicals with complex multidisciplinary technologies and theories which cover most structures feasible and thus have greatly enriched the achieve- scientific fields including chemistry, biology, pharmaceutics, ments and application scope of biocatalysis. Therefore, more and food, physics, mathematics, computer science, automation and more studies have focused on novel enzymatic reactions and engineering, and prospered the in-depth study of single-step advanced cascades for the biosynthesis of complex natural and enzymatic reactions, including enzymatic properties, reaction non-natural products, which led to a remarkable research trend mechanisms, and protein engineering. As a result, a large turning from enzymatic synthesis of compounds with simple number of enzymes used for biocatalysis have been identified structures to enzymatic total synthesis of challenging targets. from nature including almost all enzyme classes: oxidoreduc- However, since the natural synthetic pathways of many tases, transferases, hydrolases, lyases, isomerases, and ligases. natural products have not been fully elucidated, coupled with The reactions catalysed by these enzymes cover common the challenges of heterologous expression of enzymes, it is not chemical reaction types, such as redox, substitution, addition, easy to achieve the enzymatic total synthesis of natural pro- elimination, rearrangement and pericyclic reactions. Based ducts in vitro or in model host cells. Complex drug compounds on understanding enzymatic catalytic mechanisms well, these are mostly artificially designed molecular structures, which common enzymes and basic enzymatic reactions can be combined require well designed enzymatic synthesis pathways and heavy Chris Badenhorst received a BSc Shuke Wu obtained his PhD in biochemistry and microbiology from the National University of from the University of South Singapore (2015) with Prof. Zhi Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Africa. He then joined Prof. Albie Li (NUS) and Prof. Daniel I. C. van Dijk’s laboratory at the Wang (MIT). In 2017, he moved Potchefstroom Campus of the to Switzerland to work with Prof. North West University, where he Thomas R. Ward at the University obtained his BSc Honours, MSc, of Basel sponsored by a Swiss and PhD degrees in biochemistry. government excellence scholar- He was subsequently awarded an ship. Until 2020, he worked in Alexander von Humboldt Research the Bornscheuer group at the This article is licensed under a fellowship to join the Bornscheuer University of Greifswald as an Christoffel P. S. Badenhorst group, where he has been working Shuke Wu Alexander von Humboldt fellow. on the development of new Now he is a professor at the Open Access Article. Published on 18 June 2021. Downloaded 10/9/2021 12:48:46 PM. ultrahigh-throughput screening Huazhong Agricultural University methods. in China. Mark Doerr studied chemistry and Matthias Ho¨hne studied bio- biology at the Universities of chemistry and obtained his PhD Mainz and Jena. He received his in biotechnology in 2010 at PhD at the Institute of Inorganic Greifswald University under the Chemistry at the University in supervision of Prof. Uwe Jena, Germany (2004). He then Bornscheuer. He then moved to joined research projects in the Heidelberg for his postdoc to groups of Peter Nielsen in work with Prof. Andres Ja¨schke Copenhagen, Denmark (2006– and then started his Junior 2009) and Steen Rasmussen in Professorship focussing on enzyme Odense, Denmark (2009–2012) discovery and application with a working on fundamental bio-/ focus on chiral amine synthesis. Mark Doerr inorganic-chemical questions as a Matthias Ho¨hne Since 2018, he continues with an postdoctoral research associate. ERC starting grant as group leader Since 2012 he is staff scientist in the Bornscheuer group working at the Institute of Biochemistry in Greifswald and orients his research on high-throughput robotic screening, lab automation, molecular towards photobiocatalysis and the characterisation of binding and modelling and the combination of machine learning with protein transport proteins involved in marine glycan degradation. engineering. 8004 | Chem. Soc. Rev., 2021, 50, 8003–8049 This journal is © The Royal Society of Chemistry 2021 View Article Online Chem Soc Rev Review Article protein engineering to reduce the synthetic steps and solve the problem of low enzyme activity towards non-natural substrates. Comfortingly, innovative results of novel enzymes, enzymatic reaction mechanisms, and enzymatic cascades make the de novo biocatalytic synthesis of natural products and their deri- vatives easier. Especially, at present, the fourth scientific and technological revolution characterised by informatization, networking, and intellectualization is in full swing. Following Moore’s Law,3 the integration and computing power of electro- nic chips are being continuously doubled, which enable big data mining, network relational processes, and in silico protein design that require heavy computation to be realised. Machine learning (ML), which has recently entered the era of deep