1
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Bruffy SK, Meza A, Soler J, Doyon TJ, Young SH, Lim J, Huseth KG, Willoughby PH, Garcia-Borràs M, Buller AR. Biocatalytic asymmetric aldol addition into unactivated ketones. Nat Chem 2024:10.1038/s41557-024-01647-1. [PMID: 39333392 DOI: 10.1038/s41557-024-01647-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 08/29/2024] [Indexed: 09/29/2024]
Abstract
Enzymes are renowned for their catalytic efficiency and selectivity, but many classical transformations in organic synthesis have no biocatalytic counterpart. Aldolases are prodigious C-C bond-forming enzymes, but their reactivity has only been extended past activated carbonyl electrophiles in special cases. To probe the mechanistic origins of this limitation, we use a pair of aldolases whose activity is dependent on pyridoxal phosphate. Our results reveal how aldolases are limited by kinetically favourable proton transfer with solvent, which undermines aldol addition into ketones. We show how a transaldolase can circumvent this limitation, enabling efficient addition into unactivated ketones. The resulting products are highly sought non-canonical amino acids with side chains that contain chiral tertiary alcohols. Mechanistic analysis reveals that transaldolase activity is an intrinsic feature of pyridoxal phosphate chemistry and identifies principles for extending aldolase catalysis beyond its previous limits to enable convergent, enantioselective C-C bond formation from simple starting materials.
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Affiliation(s)
- Samantha K Bruffy
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Anthony Meza
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jordi Soler
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Girona, Spain
| | - Tyler J Doyon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Seth H Young
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jooyeon Lim
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathryn G Huseth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Patrick H Willoughby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, Ripon College, Ripon, WI, USA
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Girona, Spain.
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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2
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Hilvert D. Spiers Memorial Lecture: Engineering biocatalysts. Faraday Discuss 2024; 252:9-28. [PMID: 39046423 PMCID: PMC11389855 DOI: 10.1039/d4fd00139g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/25/2024]
Abstract
Enzymes are being engineered to catalyze chemical reactions for many practical applications in chemistry and biotechnology. The approaches used are surveyed in this short review, emphasizing methods for accessing reactivities not expressed by native protein scaffolds. The successful generation of completely de novo enzymes that rival the rates and selectivities of their natural counterparts highlights the potential role that designer enzymes may play in the coming years in research, industry, and medicine. Some challenges that need to be addressed to realize this ambitious dream are considered together with possible solutions.
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Affiliation(s)
- Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland.
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3
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Yu K, Ward TR. C-H functionalization reactions catalyzed by artificial metalloenzymes. J Inorg Biochem 2024; 258:112621. [PMID: 38852295 DOI: 10.1016/j.jinorgbio.2024.112621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
CH functionalization, a promising frontier in modern organic chemistry, facilitates the direct conversion of inert CH bonds into many valuable functional groups. Despite its merits, traditional homogeneous catalysis, often faces challenges in efficiency, selectivity, and sustainability towards this transformation. In this context, artificial metalloenzymes (ArMs), resulting from the incorporation of a catalytically-competent metal cofactor within an evolvable protein scaffold, bridges the gap between the efficiency of enzymatic transformations and the versatility of transition metal catalysis. Accordingly, ArMs have emerged as attractive tools for various challenging catalytic transformations. Additionally, the coming of age of directed evolution has unlocked unprecedented avenues for optimizing enzymatic catalysis. Taking advantage of their genetically-encoded protein scaffold, ArMs have been evolved to catalyze various CH functionalization reactions. This review delves into the recent developments of ArM-catalyzed CH functionalization reactions, highlighting the benefits of engineering the second coordination sphere around a metal cofactor within a host protein.
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Affiliation(s)
- Kun Yu
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4058, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4058, Switzerland.
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4
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G. Koch
- Department
of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis
Group, Institute of Chemistry, Technische
Universität Berlin, 10623 Berlin, Germany
- Chemical
Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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5
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Zhao H. Recent advances in enzymatic carbon-carbon bond formation. RSC Adv 2024; 14:25932-25974. [PMID: 39161440 PMCID: PMC11331486 DOI: 10.1039/d4ra03885a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Enzymatic carbon-carbon (C-C) bond formation reactions have become an effective and invaluable tool for designing new biological and medicinal molecules, often with asymmetric features. This review provides a systematic overview of key C-C bond formation reactions and enzymes, with the focus of reaction mechanisms and recent advances. These reactions include the aldol reaction, Henry reaction, Knoevenagel condensation, Michael addition, Friedel-Crafts alkylation and acylation, Mannich reaction, Morita-Baylis-Hillman (MBH) reaction, Diels-Alder reaction, acyloin condensations via Thiamine Diphosphate (ThDP)-dependent enzymes, oxidative and reductive C-C bond formation, C-C bond formation through C1 resource utilization, radical enzymes for C-C bond formation, and other C-C bond formation reactions.
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Affiliation(s)
- Hua Zhao
- Department of Bioproducts and Biosystems Engineering, University of Minnesota St. Paul MN 55108 USA
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6
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Zhu Z, Hu Q, Fu Y, Tong Y, Zhou Z. Design and Evolution of an Enzyme for the Asymmetric Michael Addition of Cyclic Ketones to Nitroolefins by Enamine Catalysis. Angew Chem Int Ed Engl 2024; 63:e202404312. [PMID: 38783596 DOI: 10.1002/anie.202404312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/01/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Consistent introduction of novel enzymes is required for developing efficient biocatalysts for challenging biotransformations. Absorbing catalytic modes from organocatalysis may be fruitful for designing new-to-nature enzymes with novel functions. Herein we report a newly designed artificial enzyme harboring a catalytic pyrrolidine residue that catalyzes the asymmetric Michael addition of cyclic ketones to nitroolefins through enamine activation with high efficiency. Diverse chiral γ-nitro cyclic ketones with two stereocenters were efficiently prepared with excellent stereoselectivity (up to 97 % e.e., >20 : 1 d.r.) and good yield (up to 86 %). This work provides an efficient biocatalytic strategy for cyclic ketone functionalization, and highlights the usefulness of artificial enzymes for extending biocatalysis to further non-natural reactions.
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Affiliation(s)
- Zhixi Zhu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Qinru Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Yi Fu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Yingjia Tong
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Zhi Zhou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
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7
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Noda S, Mori Y, Ogawa Y, Fujiwara R, Dainin M, Shirai T, Kondo A. Metabolic and enzymatic engineering approach for the production of 2-phenylethanol in engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 406:130927. [PMID: 38830477 DOI: 10.1016/j.biortech.2024.130927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
2-Phenylethanol, known for its rose-like odor and antibacterial activity, is synthesized via exogenous phenylpyruvate by the sequential reaction of phenylpyruvate decarboxylase (PDC) and aldehyde reductase. We first targeted ARO10, a phenylpyruvate decarboxylase gene from Saccharomyces cerevisiae, and identified a suitable aldehyde reductase gene. Co-expression of ARO10 and yahK in E. coli transformants yielded 1.1 g/L of 2-phenylethanol in batch culture. We hypothesized that there might be a bottleneck in PDC activity. The computer-based enzyme evolution was utilized to enhance production. The introduction of an amino acid substitution in ARO10 (ARO10 I544W) stabilized the aromatic ring of the phenylpyruvate substrate, increasing 2-phenylethanol yield 4.1-fold compared to wild-type ARO10. Cultivation of ARO10 I544W-expressing E. coli produced 2.5 g/L of 2-phenylethanol with a yield from glucose of 0.16 g/g after 72 h. This approach represents a significant advancement, achieving the highest yield of 2-phenylethanol from glucose using microbes to date.
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Affiliation(s)
- Shuhei Noda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; PRESTO, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
| | - Yutaro Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yuki Ogawa
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryosuke Fujiwara
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mayumi Dainin
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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8
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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9
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Wang L, Wu Y, Hu J, Yin D, Wei W, Wen J, Chen X, Gao C, Zhou Y, Liu J, Hu G, Li X, Wu J, Zhou Z, Liu L, Song W. Unlocking the function promiscuity of old yellow enzyme to catalyze asymmetric Morita-Baylis-Hillman reaction. Nat Commun 2024; 15:5737. [PMID: 38982157 PMCID: PMC11233575 DOI: 10.1038/s41467-024-50141-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Exploring the promiscuity of native enzymes presents a promising strategy for expanding their synthetic applications, particularly for catalyzing challenging reactions in non-native contexts. In this study, we explore the promiscuous potential of old yellow enzymes (OYEs) to facilitate the Morita-Baylis-Hillman reaction (MBH reaction), leveraging substrate similarities between MBH reaction and reduction reaction. Using mass spectrometry and spectroscopic techniques, we confirm promiscuity of GkOYE in both MBH and reduction reactions. By blocking H- and H+ transfer pathways, we engineer GkOYE.8, which loses its reduction ability but enhances its MBH activity. The structural basis of MBH reaction catalyzed by GkOYE.8 is obtained through mutation studies and kinetic simulations. Furthermore, enantiocomplementary mutants GkOYE.11 and GkOYE.13 are obtained by directed evolution, exhibiting the ability to accept various aromatic aldehydes and alkenes as substrates. This study demonstrates the potential of leveraging substrate similarities to unlock enzyme functionalities, enabling the catalysis of new-to-nature reactions.
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Affiliation(s)
- Lei Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yaoyun Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jun Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Dejing Yin
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Wen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yiwen Zhou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiaomin Li
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Zhi Zhou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China.
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10
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Zhou L, Tao C, Shen X, Sun X, Wang J, Yuan Q. Unlocking the potential of enzyme engineering via rational computational design strategies. Biotechnol Adv 2024; 73:108376. [PMID: 38740355 DOI: 10.1016/j.biotechadv.2024.108376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Enzymes play a pivotal role in various industries by enabling efficient, eco-friendly, and sustainable chemical processes. However, the low turnover rates and poor substrate selectivity of enzymes limit their large-scale applications. Rational computational enzyme design, facilitated by computational algorithms, offers a more targeted and less labor-intensive approach. There has been notable advancement in employing rational computational protein engineering strategies to overcome these issues, it has not been comprehensively reviewed so far. This article reviews recent developments in rational computational enzyme design, categorizing them into three types: structure-based, sequence-based, and data-driven machine learning computational design. Case studies are presented to demonstrate successful enhancements in catalytic activity, stability, and substrate selectivity. Lastly, the article provides a thorough analysis of these approaches, highlights existing challenges and potential solutions, and offers insights into future development directions.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunmeng Tao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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11
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Jain S, Ospina F, Hammer SC. A New Age of Biocatalysis Enabled by Generic Activation Modes. JACS AU 2024; 4:2068-2080. [PMID: 38938808 PMCID: PMC11200230 DOI: 10.1021/jacsau.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Biocatalysis is currently undergoing a profound transformation. The field moves from relying on nature's chemical logic to a discipline that exploits generic activation modes, allowing for novel biocatalytic reactions and, in many instances, entirely new chemistry. Generic activation modes enable a wide range of reaction types and played a pivotal role in advancing the fields of organo- and photocatalysis. This perspective aims to summarize the principal activation modes harnessed in enzymes to develop new biocatalysts. Although extensively researched in the past, the highlighted activation modes, when applied within enzyme active sites, facilitate chemical transformations that have largely eluded efficient and selective catalysis. This advance is attributed to multiple tunable interactions in the substrate binding pocket that precisely control competing reaction pathways and transition states. We will highlight cases of new synthetic methodologies achieved by engineered enzymes and will provide insights into potential future developments in this rapidly evolving field.
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Affiliation(s)
| | | | - Stephan C. Hammer
- Research Group for Organic Chemistry
and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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12
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Williams TL, Taily IM, Hatton L, Berezin AA, Wu Y, Moliner V, Świderek K, Tsai Y, Luk LYP. Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion. Angew Chem Int Ed Engl 2024; 63:e202403098. [PMID: 38545954 PMCID: PMC11497281 DOI: 10.1002/anie.202403098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Indexed: 04/20/2024]
Abstract
Secondary amines, due to their reactivity, can transform protein templates into catalytically active entities, accelerating the development of artificial enzymes. However, existing methods, predominantly reliant on modified ligands or N-terminal prolines, impose significant limitations on template selection. In this study, genetic code expansion was used to break this boundary, enabling secondary amines to be incorporated into alternative proteins and positions of choice. Pyrrolysine analogues carrying different secondary amines could be incorporated into superfolder green fluorescent protein (sfGFP), multidrug-binding LmrR and nucleotide-binding dihydrofolate reductase (DHFR). Notably, the analogue containing a D-proline moiety demonstrated both proteolytic stability and catalytic activity, conferring LmrR and DHFR with the desired transfer hydrogenation activity. While the LmrR variants were confined to the biomimetic 1-benzyl-1,4-dihydronicotinamide (BNAH) as the hydride source, the optimal DHFR variant favorably used the pro-R hydride from NADPH for stereoselective reactions (e.r. up to 92 : 8), highlighting that a switch of protein template could broaden the nucleophile option for catalysis. Owing to the cofactor compatibility, the DHFR-based secondary amine catalysis could be integrated into an enzymatic recycling scheme. This established method shows substantial potential in enzyme design, applicable from studies on enzyme evolution to the development of new biocatalysts.
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Affiliation(s)
- Thomas L. Williams
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Irshad M. Taily
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Lewis Hatton
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Andrey A Berezin
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Yi‐Lin Wu
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM)Universitat Jaume I12071CastellóSpain
| | - Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM)Universitat Jaume I12071CastellóSpain
| | - Yu‐Hsuan Tsai
- Institute of Molecular PhysiologyShenzhen Bay LaboratoryGaoke International Innovation CenterGuangming District518132Shenzhen, GuangdongChina
| | - Louis Y. P. Luk
- School of Chemistry and Cardiff Catalysis InstituteCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUnited Kingdom
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13
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Orsi E, Schada von Borzyskowski L, Noack S, Nikel PI, Lindner SN. Automated in vivo enzyme engineering accelerates biocatalyst optimization. Nat Commun 2024; 15:3447. [PMID: 38658554 PMCID: PMC11043082 DOI: 10.1038/s41467-024-46574-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization and engineering is mostly low throughput and labor-intensive. Therefore, strategies for increasing throughput while diminishing manual labor are gaining momentum, such as in vivo screening and evolution campaigns. Computational tools like machine learning further support enzyme engineering efforts by widening the explorable design space. Here, we propose an integrated solution to enzyme engineering challenges whereby ML-guided, automated workflows (including library generation, implementation of hypermutation systems, adapted laboratory evolution, and in vivo growth-coupled selection) could be realized to accelerate pipelines towards superior biocatalysts.
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Affiliation(s)
- Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | | | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany.
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, 10117, Berlin, Germany.
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14
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Thorpe T, Marshall JR, Turner NJ. Multifunctional Biocatalysts for Organic Synthesis. J Am Chem Soc 2024; 146:7876-7884. [PMID: 38489244 PMCID: PMC10979396 DOI: 10.1021/jacs.3c09542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
Biocatalysis is becoming an indispensable tool in organic synthesis due to high enzymatic catalytic efficiency as well as exquisite chemo- and stereoselectivity. Some biocatalysts display great promiscuity including a broad substrate scope as well as the ability to catalyze more than one type of transformation. These promiscuous activities have been applied individually to efficiently access numerous valuable target molecules. However, systems in which enzymes possessing multiple different catalytic activities are applied in the synthesis are less well developed. Such multifunctional biocatalysts (MFBs) would simplify chemical synthesis by reducing the number of operational steps and enzyme count, as well as simplifying the sequence space that needs to be engineered to develop an efficient biocatalyst. In this Perspective, we highlight recently reported MFBs focusing on their synthetic utility and mechanism. We also offer insight into their origin as well as comment on potential strategies for their discovery and engineering.
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Affiliation(s)
- Thomas
W. Thorpe
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
| | - James R. Marshall
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester, United Kingdom, M1
7DN
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15
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Balasubramani SG, Korchagina K, Schwartz S. Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita-Baylis-Hillman Reaction: Why Is Enzyme Design so Difficult? J Chem Inf Model 2024; 64:2101-2111. [PMID: 38451822 PMCID: PMC10963169 DOI: 10.1021/acs.jcim.4c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
It is hoped that artificial enzymes designed in laboratories can be efficient alternatives to chemical catalysts that have been used to synthesize organic molecules. However, the design of artificial enzymes is challenging and requires a detailed molecular-level analysis to understand the mechanism they promote in order to design efficient variants. In this study, we computationally investigate the mechanism of proficient Morita-Baylis-Hillman enzymes developed using a combination of computational design and directed evolution. The powerful transition path sampling method coupled with in-depth post-processing analysis has been successfully used to elucidate the different chemical pathways, transition states, protein dynamics, and free energy barriers of reactions catalyzed by such laboratory-optimized enzymes. This research provides an explanation for how different chemical modifications in an enzyme affect its catalytic activity in ways that are not predictable by static design algorithms.
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Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, Arizona 85721, United States
| | - Kseniia Korchagina
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, Arizona 85721, United States
| | - Steven Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, Arizona 85721, United States
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16
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Bell EL, Hutton AE, Burke AJ, O'Connell A, Barry A, O'Reilly E, Green AP. Strategies for designing biocatalysts with new functions. Chem Soc Rev 2024; 53:2851-2862. [PMID: 38353665 PMCID: PMC10946311 DOI: 10.1039/d3cs00972f] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Indexed: 03/19/2024]
Abstract
The engineering of natural enzymes has led to the availability of a broad range of biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and pharmaceuticals. However, for many important chemical transformations there are no known enzymes that can serve as starting templates for biocatalyst development. These limitations have fuelled efforts to build entirely new catalytic sites into proteins in order to generate enzymes with functions beyond those found in Nature. This bottom-up approach to enzyme development can also reveal new fundamental insights into the molecular origins of efficient protein catalysis. In this tutorial review, we will survey the different strategies that have been explored for designing new protein catalysts. These methods will be illustrated through key selected examples, which demonstrate how highly proficient and selective biocatalysts can be developed through experimental protein engineering and/or computational design. Given the rapid pace of development in the field, we are optimistic that designer enzymes will begin to play an increasingly prominent role as industrial biocatalysts in the coming years.
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Affiliation(s)
- Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ashleigh J Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam O'Connell
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Amber Barry
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Elaine O'Reilly
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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17
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Hutton AE, Foster J, Crawshaw R, Hardy FJ, Johannissen LO, Lister TM, Gérard EF, Birch-Price Z, Obexer R, Hay S, Green AP. A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme. Nat Commun 2024; 15:1956. [PMID: 38438341 PMCID: PMC10912507 DOI: 10.1038/s41467-024-46123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
Directed evolution of computationally designed enzymes has provided new insights into the emergence of sophisticated catalytic sites in proteins. In this regard, we have recently shown that a histidine nucleophile and a flexible arginine can work in synergy to accelerate the Morita-Baylis-Hillman (MBH) reaction with unrivalled efficiency. Here, we show that replacing the catalytic histidine with a non-canonical Nδ-methylhistidine (MeHis23) nucleophile leads to a substantially altered evolutionary outcome in which the catalytic Arg124 has been abandoned. Instead, Glu26 has emerged, which mediates a rate-limiting proton transfer step to deliver an enzyme (BHMeHis1.8) that is more than an order of magnitude more active than our earlier MBHase. Interestingly, although MeHis23 to His substitution in BHMeHis1.8 reduces activity by 4-fold, the resulting His containing variant is still a potent MBH biocatalyst. However, analysis of the BHMeHis1.8 evolutionary trajectory reveals that the MeHis nucleophile was crucial in the early stages of engineering to unlock the new mechanistic pathway. This study demonstrates how even subtle perturbations to key catalytic elements of designed enzymes can lead to vastly different evolutionary outcomes, resulting in new mechanistic solutions to complex chemical transformations.
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Affiliation(s)
- Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Jake Foster
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Rebecca Crawshaw
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Emilie F Gérard
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Richard Obexer
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK.
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18
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Zhang R, Zhang C, Tan J, He Y, Zhuo D, Zhang J, Luo Z, Li Q, Yao J, Ke C, Tang C, Ye Y, He S, Sheng X, Liao C. Enzymatic Synthesis of Noncanonical α-Amino Acids Containing γ-Tertiary Alcohols. Angew Chem Int Ed Engl 2024; 63:e202318550. [PMID: 38155101 DOI: 10.1002/anie.202318550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Noncanonical amino acids (ncAAs) containing tertiary alcohols are valuable as precursors of natural products and active pharmaceutical ingredients. However, the assembly of such ncAA scaffolds from simple material by C-C bond formation remains a challenging task due to the presence of multiple stereocenters and large steric hindrance. In this study, we present a novel solution to this problem through highly selective enzymatic decarboxylative aldol addition. This method allows for the streamlined assembly of multifunctionalized ncAAs with γ-tertiary alcohols from readily available materials, such as L -aspartatic acid and isatins, vicinal diones and keto esters. The modularity of electrophiles furnished four classes of ncAAs with decent efficiency as well as excellent site and stereocontrol. Computational modeling was employed to gain detailed insight into the catalytic mechanism and to provide a rationale for the observed selectivities. The method offers a single-step approach to producing multifunctionalized ncAAs, which can be directly utilized in peptide synthesis and bioactivity assessment.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chenghua Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, 637100, P. R. China
| | - Jiamu Tan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yifan He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Zhuo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jingxuan Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenzhen Luo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qiaoqiao Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiaying Yao
- Graduate School, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Changqiang Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chunping Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shijun He
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin, 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cangsong Liao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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19
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Chen PC, You PY, Wu LY, Chin Z, Chiu KH, Hsieh ST, Huang YW. Diastereodivergent α-Homoallylation of Cyclic Enones. Org Lett 2024. [PMID: 38181402 DOI: 10.1021/acs.orglett.3c04151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
α,β-Unsaturated carbonyls are essential structural motifs for nucleophiles of disease-related proteins. Methods for stereoselective functionalizations at the α-position include the Morita-Baylis-Hillman, Negishi, Sonogashira, Stille, and Rauhut-Currier reactions. Described here is a method for the diastereodivergent α-homoallylation of cyclic enones via a sequence of conjugate addition, aldol condensation, and diastereoselective [3,3]-sigmatropic rearrangement. Mechanistic investigations revealed that the [3,3]-sigmatropic rearrangement proceeds with transfer of chirality. These inspire a photocatalyzed olefin isomerization of the aldol condensation product leading to a highly diastereoselective [3,3]-sigmatropic rearrangement to furnish the α-homoallylation of cyclic enones. Importantly, this photocatalyzed olefin isomerization/diastereoselective [3,3]-sigmatropic rearrangement reaction sequence permits a full stereocontrol of the exo-β-position featuring an allyl group as a synthetic functional handle.
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Affiliation(s)
- Po-Chou Chen
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Pei-Yun You
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Li-Yun Wu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Zhanyi Chin
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Kuan-Hua Chiu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Song-Ting Hsieh
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
| | - Yu-Wen Huang
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
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20
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Buller R, Lutz S, Kazlauskas RJ, Snajdrova R, Moore JC, Bornscheuer UT. From nature to industry: Harnessing enzymes for biocatalysis. Science 2023; 382:eadh8615. [PMID: 37995253 DOI: 10.1126/science.adh8615] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/17/2023] [Indexed: 11/25/2023]
Abstract
Biocatalysis harnesses enzymes to make valuable products. This green technology is used in countless applications from bench scale to industrial production and allows practitioners to access complex organic molecules, often with fewer synthetic steps and reduced waste. The last decade has seen an explosion in the development of experimental and computational tools to tailor enzymatic properties, equipping enzyme engineers with the ability to create biocatalysts that perform reactions not present in nature. By using (chemo)-enzymatic synthesis routes or orchestrating intricate enzyme cascades, scientists can synthesize elaborate targets ranging from DNA and complex pharmaceuticals to starch made in vitro from CO2-derived methanol. In addition, new chemistries have emerged through the combination of biocatalysis with transition metal catalysis, photocatalysis, and electrocatalysis. This review highlights recent key developments, identifies current limitations, and provides a future prospect for this rapidly developing technology.
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Affiliation(s)
- R Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - S Lutz
- Codexis Incorporated, Redwood City, CA 94063, USA
| | - R J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - R Snajdrova
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - J C Moore
- MRL, Merck & Co., Rahway, NJ 07065, USA
| | - U T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology and Enzyme Catalysis, Greifswald University, Greifswald, Germany
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21
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Michailidou F. Engineering of Therapeutic and Detoxifying Enzymes. Angew Chem Int Ed Engl 2023; 62:e202308814. [PMID: 37433049 DOI: 10.1002/anie.202308814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/13/2023]
Abstract
Therapeutic enzymes present excellent opportunities for the treatment of human disease, modulation of metabolic pathways and system detoxification. However, current use of enzyme therapy in the clinic is limited as naturally occurring enzymes are seldom optimal for such applications and require substantial improvement by protein engineering. Engineering strategies such as design and directed evolution that have been successfully implemented for industrial biocatalysis can significantly advance the field of therapeutic enzymes, leading to biocatalysts with new-to-nature therapeutic activities, high selectivity, and suitability for medical applications. This minireview highlights case studies of how state-of-the-art and emerging methods in protein engineering are explored for the generation of therapeutic enzymes and discusses gaps and future opportunities in the field of enzyme therapy.
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Affiliation(s)
- Freideriki Michailidou
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
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22
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Chaturvedi SS, Bím D, Christov CZ, Alexandrova AN. From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics. Chem Sci 2023; 14:10997-11011. [PMID: 37860658 PMCID: PMC10583697 DOI: 10.1039/d3sc02982d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries.
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Affiliation(s)
- Shobhit S Chaturvedi
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
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23
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Zhou S, Wei Y. Kaleidoscope megamolecules synthesis and application using self-assembly technology. Biotechnol Adv 2023; 65:108147. [PMID: 37023967 DOI: 10.1016/j.biotechadv.2023.108147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 02/20/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
The megamolecules with high ordered structures play an important role in chemical biology and biomedical engineering. Self-assembly, a long-discovered but very appealing technique, could induce many reactions between biomacromolecules and organic linking molecules, such as an enzyme domain and its covalent inhibitors. Enzyme and its small-molecule inhibitors have achieved many successes in medical application, which realize the catalysis process and theranostic function. By employing the protein engineering technology, the building blocks of enzyme fusion protein and small molecule linker can be assembled into a novel architecture with the specified organization and conformation. Molecular level recognition of enzyme domain could provide both covalent reaction sites and structural skeleton for the functional fusion protein. In this review, we will discuss the range of tools available to combine functional domains by using the recombinant protein technology, which can assemble them into precisely specified architectures/valences and develop the kaleidoscope megamolecules for catalytic and medical application.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China.
| | - Yuan Wei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
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24
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Santos H, Zeoly LA, Rodrigues MT, Fernandes FS, Gomes RC, Almeida WP, Coelho F. Recent Advances in Catalytic Systems for the Mechanistically Complex Morita–Baylis–Hillman Reaction. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Hugo Santos
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Lucas A. Zeoly
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Manoel T. Rodrigues
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Fábio S. Fernandes
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Ralph C. Gomes
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Wanda P. Almeida
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Fernando Coelho
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
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25
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Wang P, Zhang J, Zhang S, Lu D, Zhu Y. Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes. J Chem Inf Model 2023; 63:1323-1337. [PMID: 36782360 DOI: 10.1021/acs.jcim.3c00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Computational enzyme design has been successfully applied to identify new alternatives to natural enzymes for the biosynthesis of important compounds. However, the moderate catalytic activities of de novo designed enzymes indicate that the modeling accuracy of current computational enzyme design methods should be improved. Here, high-throughput molecular dynamics simulations were used to enhance computational enzyme design, thus allowing the identification of variants with higher activities in silico. Different time schemes of high-throughput molecular dynamics simulations were tested to identify the catalytic features of evolved Kemp eliminases. The 20 × 1 ns molecular dynamics simulation scheme was sufficiently accurate and computationally viable to screen the computationally designed massive variants of Kemp elimination enzymes. The developed hybrid computational strategy was used to redesign the most active Kemp eliminase, HG3.17, and five variants were generated and experimentally confirmed to afford higher catalytic efficiencies than that of HG3.17, with one double variant (D52Q/A53S) exhibiting a 55% increase. The hybrid computational enzyme design strategy is general and computationally economical, with which we anticipate the efficient creation of practical enzymes for industrial biocatalysis.
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Affiliation(s)
- Pengyu Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jun Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Shengyu Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yushan Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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26
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Breukelaar W, Polidori N, Singh A, Daniel B, Glueck SM, Gruber K, Kroutil W. Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines. ACS Catal 2023; 13:2610-2618. [PMID: 36846821 PMCID: PMC9942197 DOI: 10.1021/acscatal.2c06137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/18/2023] [Indexed: 02/08/2023]
Abstract
The biocatalytic reduction of the oxime moiety to the corresponding amine group has only recently been found to be a promiscuous activity of ene-reductases transforming α-oximo β-keto esters. However, the reaction pathway of this two-step reduction remained elusive. By studying the crystal structures of enzyme oxime complexes, analyzing molecular dynamics simulations, and investigating biocatalytic cascades and possible intermediates, we obtained evidence that the reaction proceeds via an imine intermediate and not via the hydroxylamine intermediate. The imine is reduced further by the ene-reductase to the amine product. Remarkably, a non-canonical tyrosine residue was found to contribute to the catalytic activity of the ene-reductase OPR3, protonating the hydroxyl group of the oxime in the first reduction step.
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Affiliation(s)
- Willem
B. Breukelaar
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Nakia Polidori
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Amit Singh
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Bastian Daniel
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Silvia M. Glueck
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Karl Gruber
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria,Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria,BioTechMed
Graz, 8010 Graz, Austria,
| | - Wolfgang Kroutil
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria,Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria,BioTechMed
Graz, 8010 Graz, Austria,
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27
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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28
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Birch-Price Z, Taylor CJ, Ortmayer M, Green AP. Engineering enzyme activity using an expanded amino acid alphabet. Protein Eng Des Sel 2022; 36:6825271. [PMID: 36370045 PMCID: PMC9863031 DOI: 10.1093/protein/gzac013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/01/2022] [Accepted: 11/07/2022] [Indexed: 11/14/2022] Open
Abstract
Enzyme design and engineering strategies are typically constrained by the limited size of nature's genetic alphabet, comprised of only 20 canonical amino acids. In recent years, site-selective incorporation of non-canonical amino acids (ncAAs) via an expanded genetic code has emerged as a powerful means of inserting new functional components into proteins, with hundreds of structurally diverse ncAAs now available. Here, we highlight how the emergence of an expanded repertoire of amino acids has opened new avenues in enzyme design and engineering. ncAAs have been used to probe complex biological mechanisms, augment enzyme function and, most ambitiously, embed new catalytic mechanisms into protein active sites that would be challenging to access within the constraints of nature's genetic code. We predict that the studies reviewed in this article, along with further advances in genetic code expansion technology, will establish ncAA incorporation as an increasingly important tool for biocatalysis in the coming years.
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Affiliation(s)
- Zachary Birch-Price
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Christopher J Taylor
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Mary Ortmayer
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
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29
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Gutierrez-Rus LI, Alcalde M, Risso VA, Sanchez-Ruiz JM. Efficient Base-Catalyzed Kemp Elimination in an Engineered Ancestral Enzyme. Int J Mol Sci 2022; 23:8934. [PMID: 36012203 PMCID: PMC9408544 DOI: 10.3390/ijms23168934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022] Open
Abstract
The routine generation of enzymes with completely new active sites is a major unsolved problem in protein engineering. Advances in this field have thus far been modest, perhaps due, at least in part, to the widespread use of modern natural proteins as scaffolds for de novo engineering. Most modern proteins are highly evolved and specialized and, consequently, difficult to repurpose for completely new functionalities. Conceivably, resurrected ancestral proteins with the biophysical properties that promote evolvability, such as high stability and conformational diversity, could provide better scaffolds for de novo enzyme generation. Kemp elimination, a non-natural reaction that provides a simple model of proton abstraction from carbon, has been extensively used as a benchmark in de novo enzyme engineering. Here, we present an engineered ancestral β-lactamase with a new active site that is capable of efficiently catalyzing Kemp elimination. The engineering of our Kemp eliminase involved minimalist design based on a single function-generating mutation, inclusion of an extra polypeptide segment at a position close to the de novo active site, and sharply focused, low-throughput library screening. Nevertheless, its catalytic parameters (kcat/KM~2·105 M-1 s-1, kcat~635 s-1) compare favorably with the average modern natural enzyme and match the best proton-abstraction de novo Kemp eliminases that are reported in the literature. The general implications of our results for de novo enzyme engineering are discussed.
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Affiliation(s)
- Luis I. Gutierrez-Rus
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Valeria A. Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
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30
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Ding Y, Perez-Ortiz G, Peate J, Barry SM. Redesigning Enzymes for Biocatalysis: Exploiting Structural Understanding for Improved Selectivity. Front Mol Biosci 2022; 9:908285. [PMID: 35936784 PMCID: PMC9355150 DOI: 10.3389/fmolb.2022.908285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
The discovery of new enzymes, alongside the push to make chemical processes more sustainable, has resulted in increased industrial interest in the use of biocatalytic processes to produce high-value and chiral precursor chemicals. Huge strides in protein engineering methodology and in silico tools have facilitated significant progress in the discovery and production of enzymes for biocatalytic processes. However, there are significant gaps in our knowledge of the relationship between enzyme structure and function. This has demonstrated the need for improved computational methods to model mechanisms and understand structure dynamics. Here, we explore efforts to rationally modify enzymes toward changing aspects of their catalyzed chemistry. We highlight examples of enzymes where links between enzyme function and structure have been made, thus enabling rational changes to the enzyme structure to give predictable chemical outcomes. We look at future directions the field could take and the technologies that will enable it.
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31
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Abstract
The ability to design efficient enzymes from scratch would have a profound effect on chemistry, biotechnology and medicine. Rapid progress in protein engineering over the past decade makes us optimistic that this ambition is within reach. The development of artificial enzymes containing metal cofactors and noncanonical organocatalytic groups shows how protein structure can be optimized to harness the reactivity of nonproteinogenic elements. In parallel, computational methods have been used to design protein catalysts for diverse reactions on the basis of fundamental principles of transition state stabilization. Although the activities of designed catalysts have been quite low, extensive laboratory evolution has been used to generate efficient enzymes. Structural analysis of these systems has revealed the high degree of precision that will be needed to design catalysts with greater activity. To this end, emerging protein design methods, including deep learning, hold particular promise for improving model accuracy. Here we take stock of key developments in the field and highlight new opportunities for innovation that should allow us to transition beyond the current state of the art and enable the robust design of biocatalysts to address societal needs.
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32
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Ütnier T, Celebi-Olcum N. Morita-Baylis-Hillman Reaction: How Do Optimal Enzyme Active Sites Compare with Organocatalysts. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00929c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Morita-Baylis-Hillman reaction attracts significant attention for the synthesis of highly functionalized compounds. It requires multiple catalytic elements for efficient catalysis, making it an appealing target for the design of a...
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