1
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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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2
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Shan L, Li Y, Ma Y, Yang Y, Wang J, Peng L, Wang W, Zhao F, Li W, Chen X. Hairpin DNA-Based Nanomaterials for Tumor Targeting and Synergistic Therapy. Int J Nanomedicine 2024; 19:5781-5792. [PMID: 38882546 PMCID: PMC11180469 DOI: 10.2147/ijn.s461774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
Background While nanoplatform-based cancer theranostics have been researched and investigated for many years, enhancing antitumor efficacy and reducing toxic side effects is still an essential problem. Methods We exploited nanoparticle coordination between ferric (Fe2+) ions and telomerase-targeting hairpin DNA structures to encapsulate doxorubicin (DOX) and fabricated Fe2+-DNA@DOX nanoparticles (BDDF NPs). This work studied the NIR fluorescence imaging and pharmacokinetic studies targeting the ability and biodistribution of BDDF NPs. In vitro and vivo studies investigated the nano formula's toxicity, imaging, and synergistic therapeutic effects. Results The enhanced permeability and retention (EPR) effect and tumor targeting resulted in prolonged blood circulation times and high tumor accumulation. Significantly, BDDF NPs could reduce DOX-mediated cardiac toxicity by improving the antioxidation ability of cardiomyocytes based on the different telomerase activities and iron dependency in normal and tumor cells. The synergistic treatment efficacy is enhanced through Fe2+-mediated ferroptosis and the β-catenin/p53 pathway and improved the tumor inhibition rate. Conclusion Harpin DNA-based nanoplatforms demonstrated prolonged blood circulation, tumor drug accumulation via telomerase-targeting, and synergistic therapy to improve antitumor drug efficacy. Our work sheds new light on nanomaterials for future synergistic chemotherapy.
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Affiliation(s)
- Lingling Shan
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Yudie Li
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Yifan Ma
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Yang Yang
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Jing Wang
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Lei Peng
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Weiwei Wang
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Fang Zhao
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Wanrong Li
- Institute of Pharmaceutical Biotechnology, School of Biology and Food Engineering, Suzhou University, Suzhou, People's Republic of China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
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3
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Novacek A, Ugaz B, Stephanopoulos N. Templating Peptide Chemistry with Nucleic Acids: Toward Artificial Ribosomes, Cell-Specific Therapeutics, and Novel Protein-Mimetic Architectures. Biomacromolecules 2024. [PMID: 38860980 DOI: 10.1021/acs.biomac.4c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
In biology, nanomachines like the ribosome use nucleic acid templates to synthesize polymers in a sequence-specific, programmable fashion. Researchers have long been interested in using the programmable properties of nucleic acids to enhance chemical reactions via colocalization of reagents using complementary nucleic acid handles. In this review, we describe progress in using nucleic acid templates, handles, or splints to enhance the covalent coupling of peptides to other peptides or oligonucleotides. We discuss work in several areas: creating ribosome-mimetic systems, synthesizing bioactive peptides on DNA or RNA templates, linking peptides into longer molecules and bioactive antibody mimics, and scaffolding peptides to build protein-mimetic architectures. We close by highlighting the challenges that must be overcome in nucleic acid-templated peptide chemistry in two areas: making full-length, functional proteins from synthetic peptides and creating novel protein-mimetic architectures not possible through macromolecular folding alone.
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Affiliation(s)
- Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Bryan Ugaz
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
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4
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Bunyat-Zada AR, Ross AC. Highlights of bioinformatic tools and methods for validating bioinformatics derived hypotheses for microbial natural products research. Curr Opin Chem Biol 2023; 76:102367. [PMID: 37453164 DOI: 10.1016/j.cbpa.2023.102367] [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: 12/20/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Historically, bacterial natural products have served as an excellent source of drug leads, however, in recent decades the rate of discovery has slowed due to multiple challenges. Rapid advances in genome sequencing science in recent years have revealed the vast untapped encoded potential of bacteria to make natural products. To access these molecules, researchers can employ the ever-growing array of bioinformatic tools at their disposal and leverage newly developed experimental approaches to validate these bioinformatic-driven hypotheses. When used together effectively, bioinformatic and experimental tools enable researchers to deeply examine the full diversity of bacterial natural products. This review briefly outlines recent bioinformatic tools that can facilitate natural product research in bacteria including the use of CRISPR, co-occurrence network analysis, and combinatorial generation of microbial natural products to test bioinformatic hypotheses in the lab.
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Affiliation(s)
- Amir R Bunyat-Zada
- Department of Chemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON, K7L 3N6, Canada.
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5
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Zhang K, Kries H. Biomimetic engineering of nonribosomal peptide synthesis. Biochem Soc Trans 2023; 51:1521-1532. [PMID: 37409512 DOI: 10.1042/bst20221264] [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: 05/02/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/07/2023]
Abstract
Nonribosomal peptides (NRPs) have gained attention due to their diverse biological activities and potential applications in medicine and agriculture. The natural diversity of NRPs is a result of evolutionary processes that have occurred over millions of years. Recent studies have shed light on the mechanisms by which nonribosomal peptide synthetases (NRPSs) evolve, including gene duplication, recombination, and horizontal transfer. Mimicking natural evolution could be a useful strategy for engineering NRPSs to produce novel compounds with desired properties. Furthermore, the emergence of antibiotic-resistant bacteria has highlighted the urgent need for new drugs, and NRPs represent a promising avenue for drug discovery. This review discusses the engineering potential of NRPSs in light of their evolutionary history.
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Affiliation(s)
- Kexin Zhang
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena), 07745 Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena), 07745 Jena, Germany
- Organic Chemistry I, University of Bayreuth, 95440 Bayreuth, Germany
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6
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Abbood N, Effert J, Bozhueyuek KAJ, Bode HB. Guidelines for Optimizing Type S Nonribosomal Peptide Synthetases. ACS Synth Biol 2023; 12:2432-2443. [PMID: 37523786 PMCID: PMC10443035 DOI: 10.1021/acssynbio.3c00295] [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: 05/08/2023] [Indexed: 08/02/2023]
Abstract
Bacterial biosynthetic assembly lines, such as nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), play a crucial role in the synthesis of natural products that have significant therapeutic potential. The ability to engineer these biosynthetic assembly lines offers opportunities to produce artificial nonribosomal peptides, polyketides, and their hybrids with improved properties. In this study, we introduced a synthetic NRPS variant, termed type S NRPS, which simplifies the engineering process and enables biocombinatorial approaches for generating nonribosomal peptide libraries in a parallelized high-throughput manner. However, initial generations of type S NRPSs exhibited a bottleneck that led to significantly reduced production yields. To address this challenge, we employed two optimization strategies. First, we truncated SYNZIPs from the N- and/or C-terminus of the NRPS. SYNZIPs comprise a large set of well-characterized synthetic protein interaction reagents. Second, we incorporated a structurally flexible glycine-serine linker between the NRPS protein and the attached SYNZIP, aiming to improve dynamic domain-domain interactions. Through an iterative optimization process, we achieved remarkable improvements in production yields, with titer increases of up to 55-fold compared to the nonoptimized counterparts. These optimizations successfully restored production levels of type S NRPSs to those observed in wild-type NRPSs and even surpassed them. Overall, our findings demonstrate the potential of engineering bacterial biosynthetic assembly lines for the production of artificial nonribosomal peptides. In addition, optimizing the SYNZIP toolbox can have valuable implications for diverse applications in synthetic biology, such as metabolic engineering, cell signaling studies, or engineering of other multienzyme complexes, such as PKSs.
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Affiliation(s)
- Nadya Abbood
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Juliana Effert
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Kenan A. J. Bozhueyuek
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Myria
Biosciences AG, Mattenstrasse
26, 4058 Basel, Switzerland
| | - Helge B. Bode
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Chemical
Biology, Department of Chemistry, Philipps-University
Marburg, 35043 Marburg, Germany
- Senckenberg
Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
- Center for
Synthetic Microbiology (SYNMIKRO), Phillips
University Marburg, 35043 Marburg, Germany
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7
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Huang S, Ba F, Liu WQ, Li J. Stapled NRPS enhances the production of valinomycin in Escherichia coli. Biotechnol Bioeng 2023; 120:793-802. [PMID: 36510694 DOI: 10.1002/bit.28303] [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: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
Nonribosomal peptides (NRPs) are a large family of secondary metabolites with notable bioactivities, which distribute widely in natural resources across microbes and plants. To obtain these molecules, heterologous production of NRPs in robust surrogate hosts like Escherichia coli represent a feasible approach. However, reconstitution of the full biosynthetic pathway in a host often leads to low productivity, which is at least in part due to the low efficiency of enzyme interaction in vivo except for the well-known reasons of metabolic burden (e.g., expression of large NRP synthetases-NRPSs with molecular weights of >100 kDa) and cellular toxicity on host cells. To enhance the catalytic efficiency of large NRPSs in vivo, here we propose to staple NRPS enzymes by using short peptide/protein pairs (e.g., SpyTag/SpyCatcher) for enhanced NRP production. We achieve this goal by introducing a stapled NRPS system for the biosynthesis of the antibiotic NRP valinomycin in E. coli. The results indicate that stapled valinomycin synthetase (Vlm1 and Vlm2) enables higher product accumulation than those two free enzymes (e.g., the maximum improvement is nearly fourfold). After further optimization by strain and bioprocess engineering, the final valinomycin titer maximally reaches about 2800 µg/L, which is 73 times higher than the initial titer of 38 µg/L. We expect that stapling NRPS enzymes will be a promising catalytic strategy for high-level biosynthesis of NRP natural products.
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Affiliation(s)
- Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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8
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Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chem Biol 2023; 4:7-36. [PMID: 36685251 PMCID: PMC9811515 DOI: 10.1039/d2cb00169a] [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: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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9
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Tao XB, LaFrance S, Xing Y, Nava AA, Martin H, Keasling J, Backman TH. ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design. Nucleic Acids Res 2022; 51:D532-D538. [PMID: 36416273 PMCID: PMC9825560 DOI: 10.1093/nar/gkac1075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical 'starters' and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.
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Affiliation(s)
- Xavier B Tao
- Department of Chemistry, University of California, Berkeley, CA 94720, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah LaFrance
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,QB3 Institute, University of California, Berkeley, CA 94720, USA
| | - Yifei Xing
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
| | - Alberto A Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Hector Garcia Martin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,Department of Energy Agile BioFoundry, Emeryville, CA 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA,Department of Bioengineering, University of California, Berkeley, CA 94720, USA,QB3 Institute, University of California, Berkeley, CA 94720, USA,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 2800Copenhagen, Denmark,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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10
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Li Q. Geometric basis of action potential of skeletal muscle cells and neurons. Open Life Sci 2022; 17:1191-1199. [PMID: 36185399 PMCID: PMC9482420 DOI: 10.1515/biol-2022-0488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/15/2022] Open
Abstract
Although we know something about single-cell neuromuscular junctions, it is still unclear how multiple skeletal muscle cells coordinate to complete intricate spatial curve movement. Here, we hypothesize that skeletal muscle cell populations with action potentials are aligned according to curved manifolds in space (a curved shape in space). When a specific motor nerve impulse is transmitted, the skeletal muscle also moves according to the corresponding shape (manifolds). The action potential of motor nerve fibers has the characteristics of a time curve manifold, and this time-manifold curve of motor nerve fibers comes from the visual cortex in which spatial geometric manifolds are formed within the synaptic connection of neurons. This spatial geometric manifold of the synaptic connection of neurons originates from spatial geometric manifolds outside nature that are transmitted to the brain through the cone cells and ganglion cells of the retina. The essence of life is that life is an object that can move autonomously, and the essence of life's autonomous movement is the movement of proteins. Theoretically, because of the infinite diversity of geometric manifold shapes in nature, the arrangement and combination of 20 amino acids should have infinite diversity, and the geometric manifold formed by the protein three-dimensional spatial structure should also have infinite diversity.
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Affiliation(s)
- Qing Li
- Department of Function, ShiJiaZhuang Traditional Chinese Medical Hospital, No. 233, ZhongShan West Road, ShiJiaZhuang, HeBei Province 050051, China
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11
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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12
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Pourmasoumi F, De S, Peng H, Trottmann F, Hertweck C, Kries H. Proof-Reading Thioesterase Boosts Activity of Engineered Nonribosomal Peptide Synthetase. ACS Chem Biol 2022; 17:2382-2388. [PMID: 36044980 PMCID: PMC9486807 DOI: 10.1021/acschembio.2c00341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are a vast source of valuable natural products, and re-engineering them is an attractive path toward structurally diversified active compounds. NRPS engineering often requires heterologous expression, which is hindered by the enormous size of NRPS proteins. Protein splitting and docking domain insertion have been proposed as a strategy to overcome this limitation. Here, we have applied the splitting strategy to the gramicidin S NRPS: Despite better production of the split proteins, gramicidin S production almost ceased. However, the addition of type II thioesterase GrsT boosted production. GrsT is an enzyme encoded in the gramicidin S biosynthetic gene cluster that we have produced and characterized for this purpose. We attribute the activity enhancement to the removal of a stalled intermediate from the split NRPS that is formed due to misinitiation. These results highlight type II thioesterases as useful tools for NRPS engineering.
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Affiliation(s)
- Farzaneh Pourmasoumi
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sayantan De
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Huiyun Peng
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Felix Trottmann
- Biomolecular
Chemistry, Leibniz Institute for Natural
Product Research and Infection Biology e.V., Hans Knöll Institute
(HKI Jena), Beutenbergstr.
11a, 07745 Jena, Germany
| | - Christian Hertweck
- Biomolecular
Chemistry, Leibniz Institute for Natural
Product Research and Infection Biology e.V., Hans Knöll Institute
(HKI Jena), Beutenbergstr.
11a, 07745 Jena, Germany,Faculty
of Biological Sciences, Friedrich Schiller
University Jena, 07743 Jena, Germany
| | - Hajo Kries
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany,E-mail:
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13
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Toward modular construction of cell-free multienzyme systems. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(21)64002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Abbood N, Duy Vo T, Watzel J, Bozhueyuek KAJ, Bode HB. Type S Non‐Ribosomal Peptide Synthetases for the Rapid Generation of Tailormade Peptide Libraries**. Chemistry 2022; 28:e202103963. [PMID: 35176184 PMCID: PMC9315016 DOI: 10.1002/chem.202103963] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/23/2022]
Abstract
Bacterial natural products in general, and non‐ribosomally synthesized peptides in particular, are structurally diverse and provide us with a broad range of pharmaceutically relevant bioactivities. Yet, traditional natural product research suffers from rediscovering the same scaffolds and has been stigmatized as inefficient, time‐, labour‐ and cost‐intensive. Combinatorial chemistry, on the other hand, can produce new molecules in greater numbers, cheaper and in less time than traditional natural product discovery, but also fails to meet current medical needs due to the limited biologically relevant chemical space that can be addressed. Consequently, methods for the high throughput generation of new natural products would offer a new approach to identifying novel bioactive chemical entities for the hit to lead phase of drug discovery programs. As a follow‐up to our previously published proof‐of‐principle study on generating bipartite type S non‐ribosomal peptide synthetases (NRPSs), we now envisaged the de novo generation of non‐ribosomal peptides (NRPs) on an unreached scale. Using synthetic zippers, we split NRPSs in up to three subunits and rapidly generated different bi‐ and tripartite NRPS libraries to produce 49 peptides, peptide derivatives, and de novo peptides at good titres up to 145 mg L−1. A further advantage of type S NRPSs not only is the possibility to easily expand the created libraries by re‐using previously created type S NRPS, but that functions of individual domains as well as domain‐domain interactions can be studied and assigned rapidly.
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Affiliation(s)
- Nadya Abbood
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Tien Duy Vo
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Jonas Watzel
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Kenan A. J. Bozhueyuek
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Helge B. Bode
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Germany
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15
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Kinner A, Nerke P, Siedentop R, Steinmetz T, Classen T, Rosenthal K, Nett M, Pietruszka J, Lütz S. Recent Advances in Biocatalysis for Drug Synthesis. Biomedicines 2022; 10:biomedicines10050964. [PMID: 35625702 PMCID: PMC9138302 DOI: 10.3390/biomedicines10050964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 02/01/2023] Open
Abstract
Biocatalysis is constantly providing novel options for the synthesis of active pharmaceutical ingredients (APIs). In addition to drug development and manufacturing, biocatalysis also plays a role in drug discovery and can support many active ingredient syntheses at an early stage to build up entire scaffolds in a targeted and preparative manner. Recent progress in recruiting new enzymes by genome mining and screening or adapting their substrate, as well as product scope, by protein engineering has made biocatalysts a competitive tool applied in academic and industrial spheres. This is especially true for the advances in the field of nonribosomal peptide synthesis and enzyme cascades that are expanding the capabilities for the discovery and synthesis of new bioactive compounds via biotransformation. Here we highlight some of the most recent developments to add to the portfolio of biocatalysis with special relevance for the synthesis and late-stage functionalization of APIs, in order to bypass pure chemical processes.
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Affiliation(s)
- Alina Kinner
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Philipp Nerke
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Regine Siedentop
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Till Steinmetz
- Laboratory for Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (T.S.); (M.N.)
| | - Thomas Classen
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, 52428 Jülich, Germany; (T.C.); (J.P.)
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Markus Nett
- Laboratory for Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (T.S.); (M.N.)
| | - Jörg Pietruszka
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, 52428 Jülich, Germany; (T.C.); (J.P.)
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf Located at Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
- Correspondence: ; Tel.: +49-231-755-4764
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16
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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17
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Zhan S, Jiang J, Zeng Z, Wang Y, Cui H. DNA-templated coinage metal nanostructures and their applications in bioanalysis and biomedicine. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Wurlitzer JM, Stanišić A, Ziethe S, Jordan PM, Günther K, Werz O, Kries H, Gressler M. Macrophage-targeting oligopeptides from Mortierella alpina. Chem Sci 2022; 13:9091-9101. [PMID: 36091214 PMCID: PMC9365243 DOI: 10.1039/d2sc00860b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/15/2022] [Indexed: 12/27/2022] Open
Abstract
The realm of natural products of early diverging fungi such as Mortierella species is largely unexplored. Herein, the nonribosomal peptide synthetase (NRPS) MalA catalysing the biosynthesis of the surface-active biosurfactants, malpinins, has been identified and biochemically characterised. The investigation of the substrate specificity of respective adenylation (A) domains indicated a substrate-tolerant enzyme with an unusual, inactive C-terminal NRPS module. Specificity-based precursor-directed biosynthesis yielded 20 new congeners produced by a single enzyme. Moreover, MalA incorporates artificial, click-functionalised amino acids which allowed postbiosynthetic coupling to a fluorophore. The fluorescent malpinin conjugate penetrates mammalian cell membranes via an phagocytosis-mediated mechanism, suggesting Mortierella oligopeptides as carrier peptides for directed cell targeting. The current study demonstrates substrate-specificity testing as a powerful tool to identify flexible NRPS modules and highlights basal fungi as reservoir for chemically tractable compounds in pharmaceutical applications. Specificity profiling of a nonribosomal peptide synthetase of an early diverging fungus revealed high substrate flexibility. Feeding studies with click-functionalised amino acids enabled the production of fluorescent peptides targeting macrophages.![]()
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Affiliation(s)
- Jacob M. Wurlitzer
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
| | - Aleksa Stanišić
- Junior Group Biosynthetic Design of Natural Products at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Sebastian Ziethe
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
| | - Paul M. Jordan
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Kerstin Günther
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Oliver Werz
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Hajo Kries
- Junior Group Biosynthetic Design of Natural Products at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
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19
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Stanišić A, Hüsken A, Stephan P, Niquille DL, Reinstein J, Kries H. Engineered Nonribosomal Peptide Synthetase Shows Opposite Amino Acid Loading and Condensation Specificity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Aleksa Stanišić
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Annika Hüsken
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - David L. Niquille
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square NE47-140, Cambridge, Massachusetts 02139, United States
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
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20
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Dubey NC, Tripathi BP. Nature Inspired Multienzyme Immobilization: Strategies and Concepts. ACS APPLIED BIO MATERIALS 2021; 4:1077-1114. [PMID: 35014469 DOI: 10.1021/acsabm.0c01293] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.
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Affiliation(s)
- Nidhi C Dubey
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science and Engineering, Indian institute of Technology Delhi, New Delhi 110016, India
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21
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Calzini MA, Malico AA, Mitchler MM, Williams GJ. Protein engineering for natural product biosynthesis and synthetic biology applications. Protein Eng Des Sel 2021; 34:gzab015. [PMID: 34137436 PMCID: PMC8209613 DOI: 10.1093/protein/gzab015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
As protein engineering grows more salient, many strategies have emerged to alter protein structure and function, with the goal of redesigning and optimizing natural product biosynthesis. Computational tools, including machine learning and molecular dynamics simulations, have enabled the rational mutagenesis of key catalytic residues for enhanced or altered biocatalysis. Semi-rational, directed evolution and microenvironment engineering strategies have optimized catalysis for native substrates and increased enzyme promiscuity beyond the scope of traditional rational approaches. These advances are made possible using novel high-throughput screens, including designer protein-based biosensors with engineered ligand specificity. Herein, we detail the most recent of these advances, focusing on polyketides, non-ribosomal peptides and isoprenoids, including their native biosynthetic logic to provide clarity for future applications of these technologies for natural product synthetic biology.
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Affiliation(s)
- Miles A Calzini
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Alexandra A Malico
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Melissa M Mitchler
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
- Comparative Medicine Institute, NC State University Raleigh, Raleigh, NC 27695-8204, USA
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