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Petchey MR, Schneider P, Harwood LA. Biocatalytic Amino Acid Functionalisation. ChemMedChem 2025; 20:e202400628. [PMID: 39540701 DOI: 10.1002/cmdc.202400628] [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: 08/19/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/16/2024]
Abstract
The success of new therapeutic modalities relies on advancements in synthetic chemistry to produce compounds for evaluation throughout the drug discovery process. The use of non-canonical amino acids (ncAAs) allows the properties of peptide drugs to be modified and optimised beyond the defined characteristics of the 20 proteogenic amino acids. Synthesis of ncAAs can be either through a bespoke chemical synthesis, or directly from the parent compound - using either traditional chemical reagents or using enzymes - to achieve the desired modification. This review will highlight recent advancements in the enzymatic functionalisation of amino acids to produce a variety of ncAAs.
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Affiliation(s)
- Mark R Petchey
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pascal Schneider
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lucy A Harwood
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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2
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Yang D, Chiang CH, Wititsuwannakul T, Brooks CL, Zimmerman PM, Narayan ARH. Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction. J Am Chem Soc 2024; 146:34352-34363. [PMID: 39642058 PMCID: PMC11957380 DOI: 10.1021/jacs.4c08420] [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: 12/08/2024]
Abstract
Non-heme iron (FeII), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of FeII/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others. Herein, we showcase a novel ancestral sequence reconstruction (ASR)-guided strategy in which evolutionary information is used to pinpoint the residues critical for controlling different reaction pathways. Following this, a combinatorial site-directed mutagenesis approach was used to quickly evaluate the importance of each residue. These results were validated using a DNA shuffling strategy and through quantum mechanical/molecular mechanical (QM/MM) simulations. Using this approach, we identified a set of active site residues together with a key hydrogen bond between the substrate and an active site residue, which are crucial for dictating the dominant reaction pathway. Ultimately, we successfully converted both extant and ancestral enzymes that perform benzylic hydroxylation into variants that can catalyze an oxidative ring-expansion reaction, showcasing the potential of utilizing ASR to accelerate the reaction pathway engineering within enzyme families that share common structural and mechanistic features.
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Affiliation(s)
- Di Yang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States; Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chang-Hwa Chiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States; Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Charles L. Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States; Life Science Institute and Enhanced Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R. H. Narayan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States; Life Science Institute and Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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Telek A, Molnár Z, Takács K, Varga B, Grolmusz V, Tasnádi G, Vértessy BG. Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining. Appl Microbiol Biotechnol 2024; 108:101. [PMID: 38229296 PMCID: PMC10787698 DOI: 10.1007/s00253-023-12871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 01/18/2024]
Abstract
Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.
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Grants
- K119493 National Research, Development and Innovation Office
- K135231 National Research, Development and Innovation Office
- VEKOP-2.3.2-16-2017-00013 National Research, Development and Innovation Office
- NKP-2018-1.2.1-NKP-2018-00005 National Research, Development and Innovation Office
- TKP2021-EGA-02 National Research, Development and Innovation Office
- ÚNKP-22-4-II-BME-158 National Research, Development and Innovation Office
- RRF-2.3.1-21-2022-000 15 National Research, Development and Innovation Office
- C1580174 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- ELTE TKP 2021-NKTA-62 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- 2022-1.2.2-TÉT-IPARI-UZ-2022-00003 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- Budapest University of Technology and Economics
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Affiliation(s)
- András Telek
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
| | - Zsófia Molnár
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Bálint Varga
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary.
| | - Beáta G Vértessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary.
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Mao Y, Zhang W, Fu Z, Liu Y, Chen L, Lian X, Zhuo D, Wu J, Zheng M, Liao C. Versatile Biocatalytic C(sp 3 )-H Oxyfunctionalization for the Site- Selective and Stereodivergent Synthesis of α- and β-Hydroxy Acids. Angew Chem Int Ed Engl 2023; 62:e202305250. [PMID: 37340543 DOI: 10.1002/anie.202305250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/03/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
C(sp3 )-H oxyfunctionalization, the insertion of an O-atom into C(sp3 )-H bonds, streamlines the synthesis of complex molecules from easily accessible precursors and represents one of the most challenging tasks in organic chemistry with regard to site and stereoselectivity. Biocatalytic C(sp3 )-H oxyfunctionalization has the potential to overcome limitations inherent to small-molecule-mediated approaches by delivering catalyst-controlled selectivity. Through enzyme repurposing and activity profiling of natural variants, we have developed a subfamily of α-ketoglutarate-dependent iron dioxygenases that catalyze the site- and stereodivergent oxyfunctionalization of secondary and tertiary C(sp3 )-H bonds, providing concise synthetic routes towards four types of 92 α- and β-hydroxy acids with high efficiency and selectivity. This method provides a biocatalytic approach for the production of valuable but synthetically challenging chiral hydroxy acid building blocks.
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Affiliation(s)
- Yingle Mao
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
| | - Weijie Zhang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 510006, Guangzhou, China
| | - Zunyun Fu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Yanqiong Liu
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Lin Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Xin Lian
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 510006, Guangzhou, China
| | - Dan Zhuo
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Jiewei Wu
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 510006, Guangzhou, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Cangsong Liao
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
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France SP, Lewis RD, Martinez CA. The Evolving Nature of Biocatalysis in Pharmaceutical Research and Development. JACS AU 2023; 3:715-735. [PMID: 37006753 PMCID: PMC10052283 DOI: 10.1021/jacsau.2c00712] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 06/19/2023]
Abstract
Biocatalysis is a highly valued enabling technology for pharmaceutical research and development as it can unlock synthetic routes to complex chiral motifs with unparalleled selectivity and efficiency. This perspective aims to review recent advances in the pharmaceutical implementation of biocatalysis across early and late-stage development with a focus on the implementation of processes for preparative-scale syntheses.
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Zwick CR, Renata H. Overview of Amino Acid Modifications by Iron- and α-Ketoglutarate-Dependent Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Abstract
Many enzymes possess high catalytic efficiency and selectivity that far surpass classical organic or organometallic catalysts. However, the initial starting enzyme for a given transformation does not always possess the right properties needed for broad utilization. Searching in genome/protein sequence libraries for homologs, aided with powerful bioinformatic tools developed in recent years, provides an avenue to identify superior biocatalysts. Herein, we highlight several case studies to illustrate the power of this concept. A brief discussion on its complementarity with contemporary approaches in protein engineering (such as directed evolution) and possible future developments is also provided.
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Affiliation(s)
- Yanlong Jiang
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX,77005, USA
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX,77005, USA
- Lead Contact
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