1
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Sun X, Bai JK, Yang YD, Zhu KL, Liang JQ, Wang XY, Xiang JF, Hao X, Liang TL, Guan AJ, Wu NN, Gong HY. Controlled interconversion of macrocyclic atropisomers via defined intermediates. Nat Commun 2024; 15:6559. [PMID: 39095340 PMCID: PMC11297318 DOI: 10.1038/s41467-024-50739-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Macrocyclic conformations play a crucial role in regulating their properties. Our understanding of the determinants to control macrocyclic conformation interconversion is still in its infancy. Here we present a macrocycle, octamethyl cyclo[4](1,3-(4,6)-dimethylbenzene)[4]((4,6-benzene)(1,3-dicarboxylate) (OC-4), that can exist at 298 K as two stable atropisomers with C2v and C4v symmetry denoted as C2v-OC-4 and C4v-OC-4, respectively. Heating induces the efficient stepwise conversion of C2v- to C4v-OC-4 via a Cs-symmetric intermediate (Cs-OC-4). It differs from the typical transition state-mediated processes of simple C-C single bond rotations. Hydrolysis and further esterification with a countercation dependence promote the generation of C2v- and Cs-OC-4 from C4v-OC-4. In contrast to C2v-OC-4, C4v-OC-4 can bind linear guests to form pseudo-rotaxans, or bind C60 or C70 efficiently. The present study highlights the differences in recognition behavior that can result from conformational interconversion, as well as providing insights into the basic parameters that govern coupled molecular rotations.
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Affiliation(s)
- Xin Sun
- College of Chemistry, Beijing Normal University, Beijing, 100875, PR China
| | - Jin-Ku Bai
- College of Chemistry, Beijing Normal University, Beijing, 100875, PR China
| | - Yu-Dong Yang
- College of Chemistry, Beijing Normal University, Beijing, 100875, PR China
| | - Ke-Lin Zhu
- College of Chemistry, Beijing Normal University, Beijing, 100875, PR China
| | - Jia-Qi Liang
- College of Chemistry, Beijing Normal University, Beijing, 100875, PR China
| | - Xin-Yue Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, PR China
| | - Jun-Feng Xiang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiang Hao
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Tong-Ling Liang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ai-Jiao Guan
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ning-Ning Wu
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Han-Yuan Gong
- College of Chemistry, Beijing Normal University, Beijing, 100875, PR China.
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2
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Zhang Y, Saha S, Esser YCC, Ting CP. Total Synthesis and Stereochemical Assignment of Enteropeptin A. J Am Chem Soc 2024; 146:17629-17635. [PMID: 38909357 DOI: 10.1021/jacs.4c06126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
The total synthesis and structural elucidation of the antimicrobial sactipeptide enteropeptin A is reported. Enteropeptin A contains a thioaminoketal group with an unassigned stereochemical configuration that is embedded in a highly unusual thiomorpholine ring. In this synthesis, a linear peptide containing a dehydroamino acid and a pendant cysteine residue is subjected to Markovnikov hydrothiolation by a dithiophosphoric acid catalyst. This cyclization reaction forms the central thiomorpholine ring found in the enteropeptins. Both diastereomers at the unassigned thioaminoketal stereocenter of enteropeptin A were prepared, and their comparison to an authentic standard allowed for the unambiguous stereochemical assignment of the natural product to be of the D configuration. This inaugural total synthesis of enteropeptin A represents the first total synthesis of a sactipeptide reported to date. Moreover, the strategy disclosed herein serves as a general platform for the synthesis of stereochemically defined thiomorpholine-containing peptides, which may enable the discovery of new cyclic peptide antibiotics.
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Affiliation(s)
- Yiwei Zhang
- Brandeis University, Department of Chemistry, 415 South Street Waltham, Massachusetts 02453, United States
| | - Shuvendu Saha
- Brandeis University, Department of Chemistry, 415 South Street Waltham, Massachusetts 02453, United States
| | - Yannik C C Esser
- Brandeis University, Department of Chemistry, 415 South Street Waltham, Massachusetts 02453, United States
| | - Chi P Ting
- Brandeis University, Department of Chemistry, 415 South Street Waltham, Massachusetts 02453, United States
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3
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Krivoshchapov NV, Medvedev MG. Accurate and Efficient Conformer Sampling of Cyclic Drug-Like Molecules with Inverse Kinematics. J Chem Inf Model 2024; 64:4542-4552. [PMID: 38776465 DOI: 10.1021/acs.jcim.3c02040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Identification of all of the influential conformers of biomolecules is a crucial step in many tasks of computational biochemistry. Specifically, molecular docking, a key component of in silico drug development, requires a comprehensive set of conformations for potential candidates in order to generate the optimal ligand-receptor poses and, ultimately, find the best drug candidates. However, the presence of flexible cycles in a molecule complicates the initial search for conformers since exhaustive sampling algorithms via torsional random and systematic searches become very inefficient. The devised inverse-kinematics-based Monte Carlo with refinement (MCR) algorithm identifies independently rotatable dihedral angles in (poly)cyclic molecules and uses them to perform global conformational sampling, outperforming popular alternatives (MacroModel, CREST, and RDKit) in terms of speed and diversity of the resulting conformer ensembles. Moreover, MCR quickly and accurately recovers naturally occurring macrocycle conformations for most of the considered molecules.
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Affiliation(s)
- Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
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4
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Li JY, Geng YM, Rang YJ, Yang XY, Hou JY, Li CC, Yin JY. The intramolecular self-assembly of bidesmosidic kalopanaxsaponins. Nat Prod Res 2024:1-5. [PMID: 38813681 DOI: 10.1080/14786419.2024.2358391] [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: 11/16/2023] [Accepted: 05/15/2024] [Indexed: 05/31/2024]
Abstract
The phenomena of intramolecular self-assembly of bidesmosidic kalopanaxsaponins was identified for the first time in this paper. NMR (1H-NMR, NOESY), transmission electron microscopy (TEM), and molecular dynamics (MD) simulation techniques were used to compare the spatial structures of bidesmosidic kalopanaxsaponins and monodesmosidic kalopanaxsaponins. The results showed that the bidesmosidic kalopanaxsaponins formed a clustered and twisted structure in space, whereas the monodesmosidic kalopanaxsaponins were in an extended state. This discovery confirmed the presence of intramolecular self-assembly in bidesmosidic kalopanaxsaponins.
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Affiliation(s)
- Jia-Yu Li
- College of Pharmacy, Jilin University, Changchun, China
| | - Ya-Meng Geng
- College of Pharmacy, Jilin University, Changchun, China
| | - Yu-Jia Rang
- College of Pharmacy, Jilin University, Changchun, China
| | - Xin-Yu Yang
- College of Pharmacy, Jilin University, Changchun, China
| | - Jia-Yao Hou
- College of Pharmacy, Jilin University, Changchun, China
| | - Chen-Chen Li
- College of Pharmacy, Jilin University, Changchun, China
| | - Jian-Yuan Yin
- College of Pharmacy, Jilin University, Changchun, China
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5
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Abstract
Covering: 2016 to 2023Ribosomally synthesized and posttranslationally modified peptides (RiPPs) continue to be a rich source of chemically diverse and bioactive peptide natural products. In recent years, cyclophane-containing RiPP natural products and their biosynthetic pathways have been more frequently encountered. This highlight will focus on bacterial monoaryl cyclophane-containing RiPPs. This class of RiPPs is produced by radical SAM/SPASM enzymes that form a crosslink between the aromatic ring and sidechain of two amino acid residues of the precursor peptide. Selected natural products from these pathways exhibit specific antibacterial activity against gram-negative pathogens. The approaches used to discover these pathways and products will be described and categorized as natural product-first or enzyme-first. The breadth of ring systems formed by the enzymes, enzyme mechanism, and recent reports of synthetic methods for constructing these ring systems will also be presented. Bacterial cyclophane-containing RiPPs and their biosynthetic enzymes represent an untapped source of scaffolds for drug discovery and tools for synthetic biology.
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Affiliation(s)
- Chin-Soon Phan
- Department of Pharmacy, National University of Singapore, 4 Science Dr 2, Singapore 117544, Singapore.
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, 4 Science Dr 2, Singapore 117544, Singapore.
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6
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Nguyen DT, Mitchell DA, van der Donk WA. Genome Mining for New Enzyme Chemistry. ACS Catal 2024; 14:4536-4553. [PMID: 38601780 PMCID: PMC11002830 DOI: 10.1021/acscatal.3c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/12/2024]
Abstract
A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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Savoini A, Gallagher PR, Saady A, Goldup SM. The Final Stereogenic Unit of [2]Rotaxanes: Type 2 Geometric Isomers. J Am Chem Soc 2024; 146:8472-8479. [PMID: 38499387 PMCID: PMC10979452 DOI: 10.1021/jacs.3c14594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/20/2024]
Abstract
Mechanical stereochemistry arises when the interlocking of stereochemically trivial covalent subcomponents results in a stereochemically complex object. Although this general concept was identified in 1961, the stereochemical description of these molecules is still under development to the extent that new forms of mechanical stereochemistry are still being identified. Here, we present a simple analysis of rotaxane and catenane stereochemistry that allowed us to identify the final missing simple mechanical stereogenic unit, an overlooked form of rotaxane geometric isomerism, and demonstrate its stereoselective synthesis.
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Affiliation(s)
- Andrea Savoini
- School
of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K.
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Peter R. Gallagher
- School
of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K.
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Abed Saady
- School
of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K.
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Stephen M. Goldup
- School
of Chemistry, University of Southampton, University Road, Southampton SO17 1BJ, U.K.
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
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8
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Liu CL, Wang ZJ, Shi J, Yan ZY, Zhang GD, Jiao RH, Tan RX, Ge HM. P450-Modified Multicyclic Cyclophane-Containing Ribosomally Synthesized and Post-Translationally Modified Peptides. Angew Chem Int Ed Engl 2024; 63:e202314046. [PMID: 38072825 DOI: 10.1002/anie.202314046] [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: 09/19/2023] [Indexed: 01/24/2024]
Abstract
Cyclic peptides with cyclophane linkers are an attractive compound type owing to the fine-tuned rigid three-dimensional structures and unusual biophysical features. Cytochrome P450 enzymes are capable of catalyzing not only the C-C and C-O oxidative coupling reactions found in vancomycin and other nonribosomal peptides (NRPs), but they also exhibit novel catalytic activities to generate cyclic ribosomally synthesized and post-translationally modified peptides (RiPPs) through cyclophane linkage. To discover more P450-modified multicyclic RiPPs, we set out to find cryptic and unknown P450-modified RiPP biosynthetic gene clusters (BGCs) through genome mining. Synergized bioinformatic analysis reveals that P450-modified RiPP BGCs are broadly distributed in bacteria and can be classified into 11 classes. Focusing on two classes of P450-modified RiPP BGCs where precursor peptides contain multiple conserved aromatic amino acid residues, we characterized 11 novel P450-modified multicyclic RiPPs with different cyclophane linkers through heterologous expression. Further mutation of the key ring-forming residues and combinatorial biosynthesis study revealed the order of bond formation and the specificity of P450s. This study reveals the functional diversity of P450 enzymes involved in the cyclophane-containing RiPPs and indicates that P450 enzymes are promising tools for rapidly obtaining structurally diverse cyclic peptide derivatives.
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Affiliation(s)
- Cheng Li Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zi Jie Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhang Yuan Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Guo Dong Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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9
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Ye M, Li C, Xiao D, Qu G, Yuan B, Sun Z. Atroposelective Synthesis of Aldehydes via Alcohol Dehydrogenase-Catalyzed Stereodivergent Desymmetrization. JACS AU 2024; 4:411-418. [PMID: 38425895 PMCID: PMC10900225 DOI: 10.1021/jacsau.3c00814] [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: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Axially chiral aldehydes have emerged recently as a unique class of motifs for drug design. However, few biocatalytic strategies have been reported to construct structurally diverse atropisomeric aldehydes. Herein, we describe the characterization of alcohol dehydrogenases to catalyze atroposelective desymmetrization of the biaryl dialdehydes. Investigations into the interactions between the substrate and key residues of the enzymes revealed the distinct origin of atroposelectivity. A panel of 13 atropisomeric monoaldehydes was synthesized with moderate to high enantioselectivity (up to >99% ee) and yields (up to 99%). Further derivatization allows enhancement of the diversity and application potential of the atropisomeric compounds. This study effectively expands the scope of enzymatic synthesis of atropisomeric aldehydes and provides insights into the binding modes and recognition mechanisms of such molecules.
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Affiliation(s)
- Mengjing Ye
- College
of Biotechnology, Tianjin University of
Science and Technology, Tianjin 300457, China
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, China
| | - Congcong Li
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Dongguang Xiao
- College
of Biotechnology, Tianjin University of
Science and Technology, Tianjin 300457, China
| | - Ge Qu
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Bo Yuan
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Zhoutong Sun
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, China
- Key
Laboratory of Engineering Biology for Low-Carbon Manufacturing, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
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10
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Delgadillo D, Burch JE, Kim LJ, de Moraes LS, Niwa K, Williams J, Tang MJ, Lavallo VG, Khatri Chhetri B, Jones CG, Rodriguez IH, Signore JA, Marquez L, Bhanushali R, Woo S, Kubanek J, Quave C, Tang Y, Nelson HM. High-Throughput Identification of Crystalline Natural Products from Crude Extracts Enabled by Microarray Technology and microED. ACS CENTRAL SCIENCE 2024; 10:176-183. [PMID: 38292598 PMCID: PMC10823509 DOI: 10.1021/acscentsci.3c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024]
Abstract
The structural determination of natural products (NPs) can be arduous because of sample heterogeneity. This often demands iterative purification processes and characterization of complex molecules that may be available only in miniscule quantities. Microcrystal electron diffraction (microED) has recently shown promise as a method to solve crystal structures of NPs from nanogram quantities of analyte. However, its implementation in NP discovery remains hampered by sample throughput and purity requirements, akin to traditional NP-discovery workflows. In the methods described herein, we leverage the resolving power of transmission electron microscopy (TEM) and the miniaturization capabilities of deoxyribonucleic acid (DNA) microarray technology to address these challenges through the establishment of an NP screening platform, array electron diffraction (ArrayED). In this workflow, an array of high-performance liquid chromatography (HPLC) fractions taken from crude extracts was deposited onto TEM grids in picoliter-sized droplets. This multiplexing of analytes on TEM grids enables 1200 or more unique samples to be simultaneously inserted into a TEM instrument equipped with an autoloader. Selected area electron diffraction analysis of these microarrayed grids allows for the rapid identification of crystalline metabolites. In this study, ArrayED enabled structural characterization of 14 natural products, including four novel crystal structures and two novel polymorphs, from 20 crude extracts. Moreover, we identify several chemical species that would not be detected by standard mass spectrometry (MS) or ultraviolet-visible (UV/vis) spectroscopy and crystal forms that would not be characterized using traditional methods.
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Affiliation(s)
- David
A. Delgadillo
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Jessica E. Burch
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lee Joon Kim
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Lygia S. de Moraes
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Kanji Niwa
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Jason Williams
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Melody J. Tang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Vincent G. Lavallo
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Bhuwan Khatri Chhetri
- School
of Biological Sciences, School of Chemistry
and Biochemistry, and Neuroscience Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Christopher G. Jones
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Hernandez Rodriguez
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Joshua A. Signore
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lewis Marquez
- Molecular
and Systems Pharmacology, Laney Graduate School, Emory University, Atlanta, Georgia 30322, United States
| | - Riya Bhanushali
- School
of Biological Sciences, School of Chemistry
and Biochemistry, and Neuroscience Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sunmin Woo
- Center
for the Study of Human Health, Emory University, Atlanta, Georgia 30322, United States
| | - Julia Kubanek
- School
of Biological Sciences, School of Chemistry
and Biochemistry, and Neuroscience Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Cassandra Quave
- Molecular
and Systems Pharmacology, Laney Graduate School, Emory University, Atlanta, Georgia 30322, United States
- Center
for the Study of Human Health, Emory University, Atlanta, Georgia 30322, United States
- Department
of Dermatology, Emory University School
of Medicine, Atlanta, Georgia 30322, United
States
| | - Yi Tang
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Hosea M. Nelson
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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11
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Kries H, Trottmann F, Hertweck C. Novel Biocatalysts from Specialized Metabolism. Angew Chem Int Ed Engl 2024; 63:e202309284. [PMID: 37737720 DOI: 10.1002/anie.202309284] [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: 06/30/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.
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Affiliation(s)
- Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstr. 30, 95440, Bayreuth, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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12
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Yang R, Zhou Z, Jiang H, Kam TS, Chen K, Ma Z. Asymmetric Synthesis of Arboduridine. Angew Chem Int Ed Engl 2024; 63:e202316016. [PMID: 38038685 DOI: 10.1002/anie.202316016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/02/2023]
Abstract
The first asymmetric total synthesis of the monoterpenoid indole alkaloid arboduridine has been accomplished. The tricyclic A/B/D ring system was constructed by an enantioselective Michael reaction followed by intramolecular nucleophilic addition. Intramolecular α-amination of a ketone forged the piperidine ring, while a Horner-Wadsworth-Emmons (HWE) reaction was used to form the pyrrolidine ring. A reduction cyclization cascade led to formation of the tetrahydrofuran ring.
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Affiliation(s)
- Rui Yang
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry & Chemical Engineering, South China University of Technology, Wushan Road-381, Guangzhou, 510641, P. R. China
| | - Zeyu Zhou
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry & Chemical Engineering, South China University of Technology, Wushan Road-381, Guangzhou, 510641, P. R. China
| | - Huanfeng Jiang
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry & Chemical Engineering, South China University of Technology, Wushan Road-381, Guangzhou, 510641, P. R. China
| | - Toh-Seok Kam
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kai Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, P. R. China
| | - Zhiqiang Ma
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry & Chemical Engineering, South China University of Technology, Wushan Road-381, Guangzhou, 510641, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, P.R. China
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13
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Yang G, He Y, Wang T, Li Z, Wang J. Atroposelective Synthesis of Planar-Chiral Indoles via Carbene Catalyzed Macrocyclization. Angew Chem Int Ed Engl 2024; 63:e202316739. [PMID: 38014469 DOI: 10.1002/anie.202316739] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 11/29/2023]
Abstract
Indole-based planar-chiral macrocycles are widely found in natural products and bioactive molecules. However, in sharp contrast to the preparation of indole-based axially chiral structures, the enantioselective catalysis of indole-based planar-chiral macrocycles is still a formidable task so far. Here we report an N-heterocyclic carbene (NHC)-catalyzed intramolecular atroposelective macrocyclization of 3-carboxaldehyde indole/pyrroles, featuring with broad substrate scope and good functional group tolerance, and allowing for a rapid access to diverse indole/pyrrole-based planar-chiral macrocycles with various tether-lengths (10-16 members) in good yields and with excellent enantioselectivities. Importantly, the indole-based macrocyclic structures with both planar and axial chirality were directly and efficiently obtained through this protocol with excellent enantioselectivities and diastereoselectivities. In addition, these synthesized planar-chiral macrocycles offer many possibilities for chemists to develop new catalysts or ligands, as well as new reactions.
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Affiliation(s)
- Gongming Yang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Yi He
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Tianyi Wang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Zhipeng Li
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Jian Wang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
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14
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Hu YL, Yin FZ, Shi J, Ma SY, Wang ZR, Tan RX, Jiao RH, Ge HM. P450-Modified Ribosomally Synthesized Peptides with Aromatic Cross-Links. J Am Chem Soc 2023; 145:27325-27335. [PMID: 38069901 DOI: 10.1021/jacs.3c07416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cyclization of linear peptides is an effective strategy to convert flexible molecules into rigid compounds, which is of great significance for enhancing the peptide stability and bioactivity. Despite significant advances in the past few decades, Nature and chemists' ability to macrocyclize linear peptides is still quite limited. P450 enzymes have been reported to catalyze macrocyclization of peptides through cross-linkers between aromatic amino acids with only three examples. Herein, we developed an efficient workflow for the identification of P450-modified RiPPs in bacterial genomes, resulting in the discovery of a large number of P450-modified RiPP gene clusters. Combined with subsequent expression and structural characterization of the products, we have identified 11 novel P450-modified RiPPs with different cross-linking patterns from four distinct classes. Our results greatly expand the structural diversity of P450-modified RiPPs and provide new insights and enzymatic tools for the production of cyclic peptides.
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Affiliation(s)
- Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Fang Zhou Yin
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shi Ying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zi Ru Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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15
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He BB, Liu J, Cheng Z, Liu R, Zhong Z, Gao Y, Liu H, Song ZM, Tian Y, Li YX. Bacterial Cytochrome P450 Catalyzed Post-translational Macrocyclization of Ribosomal Peptides. Angew Chem Int Ed Engl 2023; 62:e202311533. [PMID: 37767859 DOI: 10.1002/anie.202311533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 09/29/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a fascinating group of natural products that exhibit diverse structural features and bioactivities. P450-catalyzed RiPPs stand out as a unique but underexplored family. Herein, we introduce a rule-based genome mining strategy that harnesses the intrinsic biosynthetic principles of RiPPs, including the co-occurrence and co-conservation of precursors and P450s and interactions between them, successfully facilitating the identification of diverse P450-catalyzed RiPPs. Intensive BGC characterization revealed four new P450s, KstB, ScnB, MciB, and SgrB, that can catalyze the formation of Trp-Trp-Tyr (one C-C and two C-N bonds), Tyr-Trp (C-C bond), Trp-Trp (C-N bond), and His-His (ether bond) crosslinks, respectively, within three or four residues. KstB, ScnB, and MciB could accept non-native precursors, suggesting they could be promising starting templates for bioengineering to construct macrocycles. Our study highlights the potential of P450s to expand the chemical diversity of strained macrocyclic peptides and the range of biocatalytic tools available for peptide macrocyclization.
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Affiliation(s)
- Bei-Bei He
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jing Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhuo Cheng
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Runze Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ying Gao
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongyan Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhi-Man Song
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongqi Tian
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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16
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Zhong G. Cytochromes P450 Associated with the Biosyntheses of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:371-388. [PMID: 37876494 PMCID: PMC10591300 DOI: 10.1021/acsbiomedchemau.3c00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 10/26/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of exponentially increased natural products with characteristic chemical structures, topologies, and biosynthetic mechanisms as well as exceptional bioactivities including antibacteria, antitumors, and antiviruses. The biosynthesis of RiPP proceeds via a ribosomally assembled precursor peptide that undergoes varied post-translational modifications to generate a mature peptide. Cytochrome P450 (CYP or P450) monooxygenases are a superfamily of heme-containing enzymes that span a wide range of secondary metabolite biosynthetic pathways due to their broad substrate scopes and excellent catalytic versatility. In contrast to the enormous quantities of RiPPs and P450s, the P450 associated RiPP biosynthesis is comparatively limited, with most of their functions and timings remaining mysterious. Herein, this Review aims to provide an overview on the striking roles of P450s in RiPP biosyntheses uncovered to date and to illustrate their remarkable functions, mechanisms, as well as remaining challenges. This will shed light on novel P450 discovery and characterizations in RiPP biosyntheses.
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Affiliation(s)
- Guannan Zhong
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute of Shandong University, Suzhou 215123, China
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17
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Nam H, An JS, Lee J, Yun Y, Lee H, Park H, Jung Y, Oh KB, Oh DC, Kim S. Exploring the Diverse Landscape of Biaryl-Containing Peptides Generated by Cytochrome P450 Macrocyclases. J Am Chem Soc 2023; 145:22047-22057. [PMID: 37756205 DOI: 10.1021/jacs.3c07140] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Cytochrome P450 enzymes (P450s) catalyze diverse oxidative cross-coupling reactions between aromatic substrates in the natural product biosynthesis. Specifically, P450s install distinct biaryl macrocyclic linkages in three families of ribosomally synthesized and post-translationally modified peptides (RiPPs). However, the chemical diversity of biaryl-containing macrocyclic RiPPs remains largely unexplored. Here, we demonstrate that P450s have the capability to generate diverse biaryl linkages on RiPPs, collectively named "cyptides". Homology-based genome mining for P450 macrocyclases revealed 19 novel groups of homologous biosynthetic gene clusters (BGCs) with distinct aromatic residue patterns in the precursor peptides. Using the P450-modified precursor peptides heterologously coexpressed with corresponding P450s in Escherichia coli, we determined the NMR structures of three novel biaryl-containing peptides─the enzymatic products, roseovertin (1), rubrin (2), and lapparbin (3)─and confirmed the formation of three unprecedented or rare biaryl linkages: Trp C-7'-to-His N-τ in 1, Trp C-7'-to-Tyr C-6 in 2, and Tyr C-6-to-Trp N-1' in 3. Biochemical characterization indicated that certain P450s in these pathways have a relaxed substrate specificity. Overall, our studies suggest that P450 macrocyclases have evolved to create diverse biaryl linkages in RiPPs, promoting the exploration of a broader chemical space for biaryl-containing peptides encoded in bacterial genomes.
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18
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An JS, Lee H, Kim H, Woo S, Nam H, Lee J, Lee JY, Nam SJ, Lee SK, Oh KB, Kim S, Oh DC. Discovery and Biosynthesis of Cihunamides, Macrocyclic Antibacterial RiPPs with a Unique C-N Linkage Formed by CYP450 Catalysis. Angew Chem Int Ed Engl 2023; 62:e202300998. [PMID: 37114290 DOI: 10.1002/anie.202300998] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023]
Abstract
Cihunamides A-D (1-4), novel antibacterial RiPPs, were isolated from volcanic-island-derived Streptomyces sp. The structures of 1-4 were elucidated by 1 H, 13 C, and 15 N NMR, MS, and chemical derivatization; they contain a tetrapeptide core composed of WNIW, cyclized by a unique C-N linkage between two Trp units. Genome mining of the producer strain revealed two biosynthetic genes encoding a cytochrome P450 enzyme and a precursor peptide. Heterologous co-expression of the core genes demonstrated the biosynthesis of cihunamides through P450-mediated oxidative Trp-Trp cross-linking. Further bioinformatic analysis uncovered 252 homologous gene clusters, including that of tryptorubins, which possess a distinct Trp-Trp linkage. Cihunamides do not display the non-canonical atropisomerism shown in tryptorubins, which are the founding members of the "atropitide" family. Therefore, we propose to use a new RiPP family name, "bitryptides", for cihunamides, tryptorubins, and their congeners, wherein the Trp-Trp linkages define the structural class rather than non-canonical atropisomerism.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Hyunbin Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Hyungyu Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Seungyeon Woo
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Hyunsung Nam
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Jayho Lee
- Department of Agriculture Biotechnology, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Ji Yun Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, College of Natural Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760 (Republic of, Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Ki-Bong Oh
- Department of Agriculture Biotechnology, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Seokhee Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
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19
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Yang P, Širvinskas MJ, Li B, Heller NW, Rong H, He G, Yudin AK, Chen G. Teraryl Braces in Macrocycles: Synthesis and Conformational Landscape Remodeling of Peptides. J Am Chem Soc 2023. [PMID: 37326500 DOI: 10.1021/jacs.3c03512] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The three-dimensional structure of medium-sized cyclic peptides accounts for their biological activity and other important physiochemical properties. Despite significant advances in the past few decades, chemists' ability to fine-tune the structure, in particular, the backbone conformation, of short peptides made of canonical amino acids is still quite limited. Nature has shown that cross-linking the aromatic side chains of linear peptide precursors via enzyme catalysis can generate cyclophane-braced products with unusual structures and diverse activities. However, the biosynthetic path to these natural products is challenging to replicate in the synthetic laboratory using practical chemical modifications of peptides. Herein, we report a broadly applicable strategy to remodel the structure of homodetic peptides by cross-linking the aromatic side chains of Trp, His, and Tyr residues with various aryl linkers. The aryl linkers can be easily installed via copper-catalyzed double heteroatom-arylation reactions of peptides with aryl diiodides. These aromatic side chains and aryl linkers can be combined to form a large variety of assemblies of heteroatom-linked multi-aryl units. The assemblies can serve as tension-bearable multijoint braces to modulate the backbone conformation of peptides as an entry to previously inaccessible conformational space.
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Affiliation(s)
- Peng Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | | | - Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Nicholas W Heller
- Department of Chemistry, University of Toronto, Toronto M5S 3H4, Canada
| | - Hua Rong
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Andrei K Yudin
- Department of Chemistry, University of Toronto, Toronto M5S 3H4, Canada
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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20
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Pairault N, Rizzi F, Lozano D, Jamieson EMG, Tizzard GJ, Goldup SM. A catenane that is topologically achiral despite being composed of oriented rings. Nat Chem 2023:10.1038/s41557-023-01194-1. [PMID: 37169983 DOI: 10.1038/s41557-023-01194-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/28/2023] [Indexed: 05/13/2023]
Abstract
Catenanes-molecules comprising two interlocking rings held together like links in a chain-are topologically non-trivial: a catenane is a topological isomer of its separated rings, but the rings cannot be disconnected without bond scission. Catenanes can exist as topological enantiomers if both rings have directionality conferred by a defined atom sequence, but this has led to the assumption that the stereochemistry of chiral catenanes composed of oriented rings is inherently topological in nature. Here we show that this assumption is incorrect by synthesizing an example that contains the same fundamental stereogenic unit but whose stereochemistry is Euclidean. One ring in this chiral catenane is oriented by the geometry of an exocyclic double rather than determined by atom sequence within the ring. Isomerization of the exocyclic double bond results in racemization of the catenane, confirming that the stereochemistry is not topological in nature. Thus, we can unite the stereochemistry of catenanes with that of their topologically trivial cousins, the rotaxanes, enabling a more unified approach to their discussion.
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Affiliation(s)
- Noel Pairault
- School of Chemistry, University of Southampton, Southampton, UK
| | - Federica Rizzi
- School of Chemistry, University of Southampton, Southampton, UK
| | - David Lozano
- School of Chemistry, University of Southampton, Southampton, UK
| | | | | | - Stephen M Goldup
- School of Chemistry, University of Southampton, Southampton, UK.
- School of Chemistry, University of Birmingham, Birmingham, UK.
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21
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Song J, Kim A, Hong I, Kim S, Byun WS, Lee HS, Kim HS, Lee SK, Kwon Y. Synthesis and biological evaluation of atropisomeric tetrahydroisoquinolines overcoming docetaxel resistance in triple-negative human breast cancer cells. Bioorg Chem 2023; 137:106573. [PMID: 37229969 DOI: 10.1016/j.bioorg.2023.106573] [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: 02/23/2023] [Revised: 04/11/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023]
Abstract
Herein, atropisomeric 8-aryltetrahydroisoquinolines have been synthesized and biologically evaluated. Based on our structure-activity relationship study, a highly bioactive racemic compound has been produced, and it exhibited high antiproliferative activities against various cancer cell lines, including docetaxel-resistant breast cancer cell lines. Each enantiomer can be synthesized in an enantioselective manner by employing the chiral phosphoric acid-catalyzed atroposelective Pictet-Spengler cyclization. An axially (R)-configured enantiomer showed a higher biological activity compared with the axially (S)-configured enantiomer. Further biological studies suggested that the (R)-enantiomer overcomes docetaxel resistance via the downregulation of signal transducer and activator of transcription 3 activation and consequently induces cellular apoptosis in docetaxel-resistant triple-negative breast cancer cell lines.
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Affiliation(s)
- Jayoung Song
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Ahreum Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Intaek Hong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sangji Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Hyung Sik Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Yongseok Kwon
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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22
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Ren H, Dommaraju SR, Huang C, Cui H, Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell DA, Zhao H. Genome mining unveils a class of ribosomal peptides with two amino termini. Nat Commun 2023; 14:1624. [PMID: 36959188 PMCID: PMC10036551 DOI: 10.1038/s41467-023-37287-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-translational modification chemistry, but genome mining of new RiPP classes remains an unsolved challenge. Here, we report a RiPP class defined by an unusual (S)-N2,N2-dimethyl-1,2-propanediamine (Dmp)-modified C-terminus, which we term the daptides. Nearly 500 daptide biosynthetic gene clusters (BGCs) were identified by analyzing the RiPP Recognition Element (RRE), a common substrate-binding domain found in half of prokaryotic RiPP classes. A representative daptide BGC from Microbacterium paraoxydans DSM 15019 was selected for experimental characterization. Derived from a C-terminal threonine residue, the class-defining Dmp is installed over three steps by an oxidative decarboxylase, aminotransferase, and methyltransferase. Daptides uniquely harbor two positively charged termini, and thus we suspect this modification could aid in membrane targeting, as corroborated by hemolysis assays. Our studies further show that the oxidative decarboxylation step requires a functionally unannotated accessory protein. Fused to the C-terminus of the accessory protein is an RRE domain, which delivers the unmodified substrate peptide to the oxidative decarboxylase. This discovery of a class-defining post-translational modification in RiPPs may serve as a prototype for unveiling additional RiPP classes through genome mining.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shravan R Dommaraju
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chunshuai Huang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Haiyang Cui
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuwei Pan
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marko Nesic
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David Sarlah
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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23
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Ren H, Dommaraju SR, Huang C, Cui H, Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell DA, Zhao H. Genome mining unveils a class of ribosomal peptides with two amino termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531785. [PMID: 36945508 PMCID: PMC10028931 DOI: 10.1101/2023.03.08.531785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-translational modification chemistry, but genome mining of new RiPP classes remains an unsolved challenge. Here, we report a RiPP class defined by an unusual ( S )- N 2 , N 2 -dimethyl-1,2-propanediamine (Dmp)-modified C -terminus, which we term the daptides. Nearly 500 daptide biosynthetic gene clusters (BGCs) were identified by analyzing the RiPP Recognition Element (RRE), a common substrate-binding domain found in half of prokaryotic RiPP classes. A representative daptide BGC from Microbacterium paraoxydans DSM 15019 was selected for experimental characterization. Derived from a C -terminal threonine residue, the class-defining Dmp is installed over three steps by an oxidative decarboxylase, aminotransferase, and methyltransferase. Daptides uniquely harbor two positively charged termini, and thus we suspect this modification could aid in membrane targeting, as corroborated by hemolysis assays. Our studies further show that the oxidative decarboxylation step requires a functionally unannotated accessory protein. Fused to the C -terminus of the accessory protein is an RRE domain, which delivers the unmodified substrate peptide to the oxidative decarboxylase. This discovery of a class-defining post-translational modification in RiPPs may serve as a prototype for unveiling additional RiPP classes through genome mining.
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24
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Bewley CA, Sulikowski GA, Yang ZJ, Bifulco G, Cho HM, Fullenkamp CR. Properties of Configurationally Stable Atropoenantiomers in Macrocyclic Natural Products and the Chrysophaentin Family. Acc Chem Res 2023; 56:414-424. [PMID: 36731116 DOI: 10.1021/acs.accounts.2c00648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
development of antibiotics, antineoplastics, and therapeutics for other diseases. Natural products are unique among all other small molecules in that they are produced by dedicated enzymatic assembly lines that are the protein products of biosynthetic gene clusters. As the products of chiral macromolecules, natural products have distinct three-dimensional shapes and stereochemistry is often encoded in their structures through the presence of stereocenters, or in the case of molecules that lack a stereocenter, the presence of an axis or plane of chirality. In the latter forms of chirality, if the barrier to rotation about the chiral axis or chiral plane is sufficiently high, stable conformers may exist allowing for isolation of discrete conformers, also known as atropisomers. Importantly, the diverse functions and biological activities of natural products are contingent upon their structures, stereochemistry and molecular shape. With continued innovation in methods for natural products discovery, synthetic chemistry, and analytical and computational tools, new insights into atropisomerism in natural products and related scaffolds are being made. As molecular complexity increases, more than one form of stereoisomerism may exist in a single compound (for example, point chirality, chiral axes, and chiral planes), sometimes creating atypical or noncanonical atropisomers, a term used to distinguish physically noninterconvertable atropisomers from typical atropisomers.Here we provide an account of the discovery and unusual structural and stereochemical features of the chrysophaentins, algal derived inhibitors of the bacterial cytoskeletal protein FtsZ and its associated protein partners. Eleven members of the chrysophaentin family have been discovered to date; seven of these are macrocyclic bis-bibenzyl ethers wherein the site of the ether linkage yields either a symmetrical or asymmetrical macrocyclic ring system. The asymmetrical ring system is highly strained and corresponds to the compounds having the most potent antimicrobial activity among the family. We review the structure elucidation and NMR properties that indicate restricted rotation between axes of two biaryl ethers, and the plane represented by the substituted 2-Z-butene bridge common to all of the macrocycles. Computational studies that corroborate high barriers to rotation about one representative plane, on the order of 20+ kcal/mol are presented. These barriers to rotation fix the conformation of the macrocycle into a bowl-like structure and suggest that an atropisomer should exist. Experimental evidence for atropisomerism is presented, consistent with computational predictions. These properties are discussed in the context of the total synthesis of 9-dechlorochrysophaenin A and its ring C isomers. Last, we discuss the implications for the presence of enantiomers in the biological activity and macrocyclization of the natural product.
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Affiliation(s)
- Carole A Bewley
- Laboratory of Bioorganic Chemistry, 8 Center Drive, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gary A Sulikowski
- Department of Chemistry, Vanderbilt University, 2213 Garland Avenue, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, 2213 Garland Avenue, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, Università di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Hyo-Moon Cho
- Laboratory of Bioorganic Chemistry, 8 Center Drive, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher R Fullenkamp
- Department of Chemistry, Vanderbilt University, 2213 Garland Avenue, Nashville, Tennessee 37235, United States
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25
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Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L. Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:1-31. [PMID: 37101606 PMCID: PMC10125368 DOI: 10.1021/acsbiomedchemau.2c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 04/28/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are of increasing interest in natural products as well as drug discovery. This empowers not only the unique chemical structures and topologies in natural products but also the excellent bioactivities such as antibacteria, antifungi, antiviruses, and so on. Advances in genomics, bioinformatics, and chemical analytics have promoted the exponential increase of RiPPs as well as the evaluation of biological activities thereof. Furthermore, benefiting from their relatively simple and conserved biosynthetic logic, RiPPs are prone to be engineered to obtain diverse analogues that exhibit distinct physiological activities and are difficult to synthesize. This Review aims to systematically address the variety of biological activities and/or the mode of mechanisms of novel RiPPs discovered in the past decade, albeit the characteristics of selective structures and biosynthetic mechanisms are briefly covered as well. Almost one-half of the cases are involved in anti-Gram-positive bacteria. Meanwhile, an increasing number of RiPPs related to anti-Gram-negative bacteria, antitumor, antivirus, etc., are also discussed in detail. Last but not least, we sum up some disciplines of the RiPPs' biological activities to guide genome mining as well as drug discovery and optimization in the future.
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Affiliation(s)
- Guannan Zhong
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
| | - Zong-Jie Wang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fu Yan
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS
Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liujie Huo
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
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26
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Zhao JX, Yue JM. Frontier studies on natural products: moving toward paradigm shifts. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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27
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Biermann F, Wenski SL, Helfrich EJN. Navigating and expanding the roadmap of natural product genome mining tools. Beilstein J Org Chem 2022; 18:1656-1671. [PMID: 36570563 PMCID: PMC9749553 DOI: 10.3762/bjoc.18.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Natural products are structurally highly diverse and exhibit a wide array of biological activities. As a result, they serve as an important source of new drug leads. Traditionally, natural products have been discovered by bioactivity-guided fractionation. The advent of genome sequencing technology has resulted in the introduction of an alternative approach towards novel natural product scaffolds: Genome mining. Genome mining is an in-silico natural product discovery strategy in which sequenced genomes are analyzed for the potential of the associated organism to produce natural products. Seemingly universal biosynthetic principles have been deciphered for most natural product classes that are used to detect natural product biosynthetic gene clusters using pathway-encoded conserved key enzymes, domains, or motifs as bait. Several generations of highly sophisticated tools have been developed for the biosynthetic rule-based identification of natural product gene clusters. Apart from these hard-coded algorithms, multiple tools that use machine learning-based approaches have been designed to complement the existing genome mining tool set and focus on natural product gene clusters that lack genes with conserved signature sequences. In this perspective, we take a closer look at state-of-the-art genome mining tools that are based on either hard-coded rules or machine learning algorithms, with an emphasis on the confidence of their predictions and potential to identify non-canonical natural product biosynthetic gene clusters. We highlight the genome mining pipelines' current strengths and limitations by contrasting their advantages and disadvantages. Moreover, we introduce two indirect biosynthetic gene cluster identification strategies that complement current workflows. The combination of all genome mining approaches will pave the way towards a more comprehensive understanding of the full biosynthetic repertoire encoded in microbial genome sequences.
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Affiliation(s)
- Friederike Biermann
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Sebastian L Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Eric J N Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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28
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He B, Cheng Z, Zhong Z, Gao Y, Liu H, Li Y. Expanded Sequence Space of Radical S‐Adenosylmethionine‐Dependent Enzymes Involved in Post‐translational Macrocyclization**. Angew Chem Int Ed Engl 2022; 61:e202212447. [DOI: 10.1002/anie.202212447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Bei‐Bei He
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China
| | - Zhuo Cheng
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
| | - Ying Gao
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China
| | - Hongyan Liu
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China
| | - Yong‐Xin Li
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China
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29
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Han EJ, Lee SR, Hoshino S, Seyedsayamdost MR. Targeted Discovery of Cryptic Metabolites with Antiproliferative Activity. ACS Chem Biol 2022; 17:3121-3130. [PMID: 36228140 PMCID: PMC10171914 DOI: 10.1021/acschembio.2c00588] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microorganisms have provided a rich source of therapeutically valuable natural products. Recent advances in whole genome sequencing and bioinformatics have revealed immense untapped potential for new natural products in the form of silent or "cryptic" biosynthetic genes. We herein conducted high-throughput elicitor screening (HiTES) in conjunction with cytotoxicity assays against selected cancer cell lines with the goal of uncovering otherwise undetectable cryptic metabolites with antiproliferative activity. Application to Streptomyces clavuligerus facilitated identification of clavamates A and B, two bioactive metabolites with unusual structural features, as well as facile activation of a gene cluster coding for tunicamycin, which exhibited strong growth-inhibitory activity. The elicitor we identified was pleiotropic, additionally leading to the discovery of a modified, bicyclic pentapeptide natural product. Our results highlight the utility of this approach in identifying new molecules with antiproliferative activity from even overexploited microbial strains.
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Affiliation(s)
- Esther J. Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- These authors contributed equally
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- These authors contributed equally
| | - Shotaro Hoshino
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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30
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Total synthesis of (+)-asperazine A: A stereoselective domino dimerization. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Yao G, Kosol S, Wenz MT, Irran E, Keller BG, Trapp O, Süssmuth RD. The occurrence of ansamers in the synthesis of cyclic peptides. Nat Commun 2022; 13:6488. [PMID: 36310176 PMCID: PMC9618573 DOI: 10.1038/s41467-022-34125-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
α-Amanitin is a bicyclic octapeptide composed of a macrolactam with a tryptathionine cross-link forming a handle. Previously, the occurrence of isomers of amanitin, termed atropisomers has been postulated. Although the total synthesis of α-amanitin has been accomplished this aspect still remains unsolved. We perform the synthesis of amanitin analogs, accompanied by in-depth spectroscopic, crystallographic and molecular dynamics studies. The data unambiguously confirms the synthesis of two amatoxin-type isomers, for which we propose the term ansamers. The natural structure of the P-ansamer can be ansa-selectively synthesized using an optimized synthetic strategy. We believe that the here described terminology does also have implications for many other peptide structures, e.g. norbornapeptides, lasso peptides, tryptorubins and others, and helps to unambiguously describe conformational isomerism of cyclic peptides.
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Affiliation(s)
- Guiyang Yao
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany ,grid.8547.e0000 0001 0125 2443Center for Innovative Drug Discovery, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Shanghai, PR China
| | - Simone Kosol
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Marius T. Wenz
- grid.14095.390000 0000 9116 4836Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Elisabeth Irran
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Bettina G. Keller
- grid.14095.390000 0000 9116 4836Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Oliver Trapp
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany ,grid.429508.20000 0004 0491 677XMax-Planck-Institute for Astronomy, Königstuhl 17, 69117 Heidelberg, Germany
| | - Roderich D. Süssmuth
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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32
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Laws D, Plouch EV, Blakey SB. Synthesis of Ribosomally Synthesized and Post-Translationally Modified Peptides Containing C-C Cross-Links. JOURNAL OF NATURAL PRODUCTS 2022; 85:2519-2539. [PMID: 36136399 PMCID: PMC9617794 DOI: 10.1021/acs.jnatprod.2c00508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are known for their macrocyclic structures, which impart unique biological activity. One rapidly emerging subclass of RiPP natural products contains macrocyclic C-C cross-links between two amino acid side chains. These linkages, often biosynthetically formed by a single rSAM or P450 enzyme, introduce significant structural and synthetic complexity to the molecules. While nature utilizes elegant mechanisms to produce C-C cross-linked RiPPs, synthetic tools are only able to access a portion of these biologically relevant natural products. This review provides an overview of the structures in this subclass as well as a discussion on their chemical syntheses.
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Affiliation(s)
- David Laws
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Eleda V Plouch
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Simon B Blakey
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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33
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Yang X, Lim SHM, Lin J, Wu J, Tang H, Zhao F, Liu F, Sun C, Shi X, Kuang Y, Toy JYH, Du K, Zhang Y, Wang X, Sun M, Song Z, Wang T, Wu J, Houk KN, Huang D. Oxygen mediated oxidative couplings of flavones in alkaline water. Nat Commun 2022; 13:6424. [PMID: 36307433 PMCID: PMC9614196 DOI: 10.1038/s41467-022-34123-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Catalyzed oxidative C-C bond coupling reactions play an important role in the chemical synthesis of complex natural products of medicinal importance. However, the poor functional group tolerance renders them unfit for the synthesis of naturally occurring polyphenolic flavones. We find that molecular oxygen in alkaline water acts as a hydrogen atom acceptor and oxidant in catalyst-free (without added catalyst) oxidative coupling of luteolin and other flavones. By this facile method, we achieve the synthesis of a small collection of flavone dimers and trimers including naturally occurring dicranolomin, philonotisflavone, dehydrohegoflavone, distichumtriluteolin, and cyclodistichumtriluteolin. Mechanistic studies using both experimental and computational chemistry uncover the underlying reasons for optimal pH, oxygen availability, and counter-cations that define the success of the reaction. We expect our reaction opens up a green and sustainable way to synthesize flavonoid dimers and oligomers using the readily available monomeric flavonoids isolated from biomass and exploiting their use for health care products and treatment of diseases.
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Affiliation(s)
- Xin Yang
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Sophie Hui Min Lim
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Jiachen Lin
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Jie Wu
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Republic of Singapore ,grid.452673.1National University of Singapore (Suzhou) Research Institute, 377 Linquan Street, 215123 Suzhou, Jiangsu China
| | - Haidi Tang
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Republic of Singapore ,grid.452673.1National University of Singapore (Suzhou) Research Institute, 377 Linquan Street, 215123 Suzhou, Jiangsu China
| | - Fengyue Zhao
- grid.27871.3b0000 0000 9750 7019College of Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fang Liu
- grid.27871.3b0000 0000 9750 7019College of Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Chenghua Sun
- grid.1027.40000 0004 0409 2862Department of Chemistry and Biotechnology, FSET, Swinburne University of Technology, Hawthorn, VIC 3122 Australia
| | - Xiangcheng Shi
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Republic of Singapore
| | - Yulong Kuang
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Republic of Singapore
| | - Joanne Yi Hui Toy
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Ke Du
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Yuannian Zhang
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Xiang Wang
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Mingtai Sun
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Zhixuan Song
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore
| | - Tian Wang
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Republic of Singapore
| | - Ji’en Wu
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Republic of Singapore
| | - K. N. Houk
- grid.19006.3e0000 0000 9632 6718Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Dejian Huang
- grid.4280.e0000 0001 2180 6431Department of Food Science and Technology, National University of Singapore, 2 Science Drive 2, Singapore, 117542 Republic of Singapore ,grid.452673.1National University of Singapore (Suzhou) Research Institute, 377 Linquan Street, 215123 Suzhou, Jiangsu China
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34
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Weng Y, Xu X, Chen H, Zhang Y, Zhuo X. Tandem Electrochemical Oxidative Azidation/Heterocyclization of Tryptophan‐Containing Peptides under Buffer Conditions. Angew Chem Int Ed Engl 2022; 61:e202206308. [DOI: 10.1002/anie.202206308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Yiyi Weng
- College of Pharmaceutical Sciences Zhejiang University of Technology 310014 Hangzhou P.R. China
| | - Xiaobin Xu
- College of Pharmaceutical Sciences Zhejiang University of Technology 310014 Hangzhou P.R. China
| | - Hantao Chen
- College of Pharmaceutical Sciences Zhejiang University of Technology 310014 Hangzhou P.R. China
| | - Yiyang Zhang
- College of Pharmaceutical Sciences Zhejiang University of Technology 310014 Hangzhou P.R. China
| | - Xianfeng Zhuo
- College of Pharmaceutical Sciences Zhejiang University of Technology 310014 Hangzhou P.R. China
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35
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Nanudorn P, Thiengmag S, Biermann F, Erkoc P, Dirnberger SD, Phan TN, Fürst R, Ueoka R, Helfrich EJN. Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape. Angew Chem Int Ed Engl 2022; 61:e202208361. [PMID: 35939298 PMCID: PMC9826248 DOI: 10.1002/anie.202208361] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 01/11/2023]
Abstract
Biomacromolecules are known to feature complex three-dimensional shapes that are essential for their function. Among natural products, ambiguous molecular shapes are a rare phenomenon. The hexapeptide tryptorubin A can adopt one of two unusual atropisomeric configurations. Initially hypothesized to be a non-ribosomal peptide, we show that tryptorubin A is the first characterized member of a new family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) that we named atropopeptides. The sole modifying enzyme encoded in the gene cluster, a cytochrome P450 monooxygenase, is responsible for the atropospecific formation of one carbon-carbon and two carbon-nitrogen bonds. The characterization of two additional atropopeptide biosynthetic pathways revealed a two-step maturation process. Atropopeptides promote pro-angiogenic cell functions as indicated by an increase in endothelial cell proliferation and undirected migration. Our study expands the biochemical space of RiPP-modifying enzymes and paves the way towards the chemoenzymatic utilization of atropopeptide-modifying P450s.
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Affiliation(s)
- Pakjira Nanudorn
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Friederike Biermann
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Pelin Erkoc
- LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany,Institute of Pharmaceutical BiologyGoethe University FrankfurtMax-von-Laue Strasse 960438FrankfurtGermany
| | - Sabrina D. Dirnberger
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Thao N. Phan
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Robert Fürst
- LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany,Institute of Pharmaceutical BiologyGoethe University FrankfurtMax-von-Laue Strasse 960438FrankfurtGermany
| | - Reiko Ueoka
- School of Marine BiosciencesKitasato University1-15-1 Kitasato, Minami-kuSagamiharaKanagawa, 252-0373Japan
| | - Eric J. N. Helfrich
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
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36
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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37
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Yang P, Li YY, Tian H, Qian GL, Wang Y, Hong X, Gui J. Syntheses of Bufospirostenin A and Ophiopogonol A by a Conformation-Controlled Transannular Prins Cyclization. J Am Chem Soc 2022; 144:17769-17775. [PMID: 36125970 DOI: 10.1021/jacs.2c07944] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Controlling the conformation of medium-sized rings is challenging because of their flexibility and ring strain effects. Herein, we report non-Curtin-Hammett conditions for the precise control of the conformation of cyclodecenones to effect the first cis-selective transannular Prins cyclization, which enabled concise syntheses of the 5(10→1)abeo-steroids bufospirostenin A and ophiopogonol A in only seven steps from inexpensive starting materials. Computational results indicated that the key cyclization was kinetically controlled and proceeded via either a Prins pathway or a carbonyl-ene pathway, depending on the reaction conditions. Moreover, conformational isomerization played a critical role in determining the stereochemistry of the products.
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Affiliation(s)
- Peicheng Yang
- Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.,CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yan-Yu Li
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
| | - Hailong Tian
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gan-Lu Qian
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
| | - Yun Wang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China.,Beijing National Laboratory for Molecular Sciences, Zhongguancun North First Street No. 2, Beijing 100190, PR China.,Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Jinghan Gui
- Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.,CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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38
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450 Blt Enables Versatile Peptide Cyclisation to Generate Histidine- and Tyrosine-Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022; 61:e202204957. [PMID: 35851739 PMCID: PMC9542247 DOI: 10.1002/anie.202204957] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 12/05/2022]
Abstract
We report our investigation of the utility of peptide crosslinking cytochrome P450 enzymes from biarylitide biosynthesis to generate a range of cyclic tripeptides from simple synthons. The crosslinked tripeptides produced by this P450 include both tyrosine-histidine (A-N-B) and tyrosine-tryptophan (A-O-B) crosslinked tripeptides, the latter a rare example of a phenolic crosslink to an indole moiety. Tripeptides are easily isolated following proteolytic removal of the leader peptide and can incorporate a wide range of amino acids in the residue inside the crosslinked tripeptide. Given the utility of peptide crosslinks in important natural products and the synthetic challenge that these can represent, P450 enzymes have the potential to play roles as important tools in the generation of high-value cyclic tripeptides for incorporation in synthesis, which can be yet further diversified using selective chemical techniques through specific handles contained within these tripeptides.
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Affiliation(s)
- Yongwei Zhao
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Maxine Treisman
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Alasdair McKay
- Department of ChemistryMonash UniversityClaytonVIC 3800Australia
| | - Leo Padva
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of TennesseeMemphisTN 38163USA
| | - David L. Steer
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
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39
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Maynard JR, Gallagher P, Lozano D, Butler P, Goldup SM. Mechanically axially chiral catenanes and noncanonical mechanically axially chiral rotaxanes. Nat Chem 2022; 14:1038-1044. [PMID: 35760959 PMCID: PMC7613450 DOI: 10.1038/s41557-022-00973-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/12/2022] [Indexed: 12/30/2022]
Abstract
Chirality typically arises in molecules because of a rigidly chiral arrangement of covalently bonded atoms. Less generally appreciated is that chirality can arise when molecules are threaded through one another to create a mechanical bond. For example, when two macrocycles with chemically distinct faces are joined to form a catenane, the structure is chiral, although the rings themselves are not. However, enantiopure mechanically axially chiral catenanes in which the mechanical bond provides the sole source of stereochemistry have not been reported. Here we re-examine the symmetry properties of these molecules and in doing so identify a straightforward route to access them from simple chiral building blocks. Our analysis also led us to identify an analogous but previously unremarked upon rotaxane stereogenic unit, which also yielded to our co-conformational auxiliary approach. With methods to access mechanically axially chiral molecules in hand, their properties and applications can now be explored.
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40
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Weng Y, Xu X, Chen H, Zhang Y, Zhuo X. Tandem Electrochemical Oxidative Azidation/Heterocyclization of Tryptophan‐Containing Peptides under Buffer Conditions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yiyi Weng
- Zhejiang University of Technology College of Pharmaceutical Science Chaowang road 18 310014 Hangzhou CHINA
| | - Xiaobin Xu
- Zhejiang University of Technology College of Pharmaceutical Sciences CHINA
| | - Hantao Chen
- Zhejiang University of Technology College of Pharmaceutical Sciences CHINA
| | - Yiyang Zhang
- Zhejiang University of Technology College of Pharmaceutical Sciences CHINA
| | - Xianfeng Zhuo
- Zhejiang University of Technology College of Pharmaceutical Sciences CHINA
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41
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Lin YC, Schneider F, Eberle KJ, Chiodi D, Nakamura H, Reisberg SH, Chen J, Saito M, Baran PS. Atroposelective Total Synthesis of Darobactin A. J Am Chem Soc 2022; 144:14458-14462. [PMID: 35926121 PMCID: PMC9829381 DOI: 10.1021/jacs.2c05892] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A concise, modular synthesis of the novel antibiotic darobactin A is disclosed. The synthesis successfully forges the hallmark strained macrocyclic ring systems in a sequential fashion. Key transformations include two atroposelective Larock-based macrocyclizations, one of which proceeds with exquisite regioselectivity despite bearing an unprotected alkyne. The synthesis is designed with medicinal chemistry considerations in mind, appending key portions of the molecule at a late stage. Requisite unnatural amino acid building blocks are easily prepared in an enantiopure form using C-H activation and decarboxylative cross-coupling tactics.
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Affiliation(s)
- You-Chen Lin
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Fabian Schneider
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kelly J Eberle
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Debora Chiodi
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hugh Nakamura
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Solomon H Reisberg
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jason Chen
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Masato Saito
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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42
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Nanudorn P, Thiengmag S, Biermann F, Erkoc P, Dirnberger SD, Phan TN, Fürst R, Ueoka R, Helfrich EJN. Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pakjira Nanudorn
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Sirinthra Thiengmag
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Friederike Biermann
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Pelin Erkoc
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute of Pharmaceutical Biology Biozentrum Building 230Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Sabrina Doris Dirnberger
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Thao Ngoc Phan
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Robert Fürst
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute of Pharmaceutical Biology Biozentrum Building 230Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Reiko Ueoka
- Kitasato University: Kitasato Daigaku School of Marine Biosciences 1-15-1 KitasatoMinami-kuSagamihara 252-0373 Kanagawa JAPAN
| | - Eric Jan Nikolaus Helfrich
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
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43
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450Blt Enables Versatile Peptide Cyclisation to Generate Histidine and Tyrosine Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | | | - Leo Padva
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Pharmaceutical Biology GERMANY
| | - Max Crüsemann
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Pharmaceutical Biology GERMANY
| | - David R Nelson
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Microbiology UNITED STATES
| | - David L Steer
- Monash University Biochemistry and Molecular Biology AUSTRALIA
| | | | | | - Max J. Cryle
- Monash University Department of Biochemistry and Molecular Biology 15 Innovation WalkMonash University 3800 Melbourne AUSTRALIA
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44
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Sun C, Tian W, Lin Z, Qu X. Biosynthesis of pyrroloindoline-containing natural products. Nat Prod Rep 2022; 39:1721-1765. [PMID: 35762180 DOI: 10.1039/d2np00030j] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022Pyrroloindoline is a privileged tricyclic indoline motif widely present in many biologically active and medicinally valuable natural products. Thus, understanding the biosynthesis of this molecule is critical for developing convenient synthetic routes, which is highly challenging for its chemical synthesis due to the presence of rich chiral centers in this molecule, especially the fully substituted chiral carbon center at the C3-position of its rigid tricyclic structure. In recent years, progress has been made in elucidating the biosynthetic pathways and enzymatic mechanisms of pyrroloindoline-containing natural products (PiNPs). This article reviews the main advances in the past few decades based on the different substitutions on the C3 position of PiNPs, especially the various key enzymatic mechanisms involved in the biosynthesis of different types of PiNPs.
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Affiliation(s)
- Chenghai Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xudong Qu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
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45
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Rodríguez-Rubio A, Savoini A, Modicom F, Butler P, Goldup SM. A Co-conformationally "Topologically" Chiral Catenane. J Am Chem Soc 2022; 144:11927-11932. [PMID: 35763555 PMCID: PMC9348828 DOI: 10.1021/jacs.2c02029] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Catenanes composed of two achiral rings that are oriented (Cnh symmetry) because of the sequence of atoms they contain are referred to as topologically chiral. Here, we present the synthesis of a highly enantioenriched catenane containing a related but overlooked "co-conformationally 'topologically' chiral" stereogenic unit, which arises when a bilaterally symmetric Cnv ring is desymmetrized by the position of an oriented macrocycle.
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Affiliation(s)
- Arnau Rodríguez-Rubio
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Andrea Savoini
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Florian Modicom
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Patrick Butler
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Stephen M Goldup
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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46
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Abstract
The past decade has seen impressive advances in understanding the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs). One of the most common modifications found in these natural products is macrocyclization, a strategy also used by medicinal chemists to improve metabolic stability and target affinity and specificity. Another tool of the peptide chemist, modification of the amides in a peptide backbone, has also been observed in RiPPs. This review discusses the molecular mechanisms of biosynthesis of a subset of macrocyclic RiPP families, chosen because of the unusual biochemistry involved: the five classes of lanthipeptides (thioether cyclization by Michael-type addition), sactipeptides and ranthipeptides (thioether cyclization by radical chemistry), thiopeptides (cyclization by [4+2] cycloaddition), and streptide (cyclization by radical C-C bond formation). In addition, the mechanisms of backbone amide methylation, backbone epimerization, and backbone thioamide formation are discussed, as well as an unusual route to small molecules by posttranslational modification.
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Affiliation(s)
- Hyunji Lee
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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47
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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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48
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Bertuzzi G, Corti V, Izzo JA, Ričko S, Jessen NI, Jørgensen KA. Organocatalytic Enantioselective Construction of Conformationally Stable C(sp 2)-C(sp 3) Atropisomers. J Am Chem Soc 2022; 144:1056-1065. [PMID: 34990550 DOI: 10.1021/jacs.1c12619] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonbiaryl atropisomers are molecules defined by a stereogenic axis featuring at least one nonarene moiety. Among these, scaffolds bearing a conformationally stable C(sp2)-C(sp3) stereogenic axis have been observed in natural compounds; however, their enantioselective synthesis remains almost completely unexplored. Herein we disclose a new class of chiral C(sp2)-C(sp3) atropisomers obtained with high levels of stereoselectivity (up to 99% ee) by means of an organocatalytic asymmetric methodology. Multiple molecular motifs could be embedded in this class of C(sp2)-C(sp3) atropisomers, showing a broad and general protocol. Experimental data provide strong evidence of the conformational stability of the C(sp2)-C(sp3) stereogenic axis (up to t1/225 °C >1000 y) in the obtained compounds and show kinetic control over this rare stereogenic element. This, coupled with density functional theory calculations, suggests that the observed stereoselectivity arises from a Curtin-Hammett scenario establishing an equilibrium of intermediates. Furthermore, the experimental investigation led to evidence of the operating principle of central-to-axial chirality conversions.
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Affiliation(s)
- Giulio Bertuzzi
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Vasco Corti
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Joseph A Izzo
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sebastijan Ričko
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
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Ramesh S, Guo X, DiCaprio AJ, De Lio AM, Harris LA, Kille BL, Pogorelov TV, Mitchell DA. Bioinformatics-Guided Expansion and Discovery of Graspetides. ACS Chem Biol 2021; 16:2787-2797. [PMID: 34766760 DOI: 10.1021/acschembio.1c00672] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products featuring ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications arise from serine, threonine, or lysine donor residues linked to aspartate or glutamate acceptor residues. Characterized graspetides include serine protease inhibitors such as the microviridins and plesiocin. Here, we report an update to Rapid ORF Description and Evaluation Online (RODEO) for the automated detection of graspetides, which identified 3,923 high-confidence graspetide biosynthetic gene clusters. Sequence and co-occurrence analyses doubled the number of graspetide groups from 12 to 24, defined based on core consensus sequence and putative secondary modification. Bioinformatic analyses of the ATP-grasp ligase superfamily suggest that extant graspetide synthetases diverged once from an ancestral ATP-grasp ligase and later evolved to introduce a variety of ring connectivities. Furthermore, we characterized thatisin and iso-thatisin, two graspetides related by conformational stereoisomerism from Lysobacter antibioticus. Derived from a newly identified graspetide group, thatisin and iso-thatisin feature two interlocking macrolactones with identical ring connectivity, as determined by a combination of tandem mass spectrometry (MS/MS), methanolytic, and mutational analyses. NMR spectroscopy of thatisin revealed a cis conformation for a key proline residue, while molecular dynamics simulations, solvent-accessible surface area calculations, and partial methanolytic analysis coupled with MS/MS support a trans conformation for iso-thatisin at the same position. Overall, this work provides a comprehensive overview of the graspetide landscape, and the improved RODEO algorithm will accelerate future graspetide discoveries by enabling open-access analysis of existing and emerging genomes.
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Affiliation(s)
- Sangeetha Ramesh
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Xiaorui Guo
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Adam J. DiCaprio
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ashley M. De Lio
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
| | - Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Bryce L. Kille
- Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Swain JA, Walker SR, Calvert MB, Brimble MA. The tryptophan connection: cyclic peptide natural products linked via the tryptophan side chain. Nat Prod Rep 2021; 39:410-443. [PMID: 34581375 DOI: 10.1039/d1np00043h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: from 1938 up to March 2021The electron-rich indole side chain of tryptophan is a versatile substrate for peptide modification. Upon the action of various cyclases, the tryptophan side chain may be linked to a nearby amino acid residue, opening the door to a diverse range of cyclic peptide natural products. These compounds exhibit a wide array of biological activity and possess fascinating molecular architectures, which have made them popular targets for total synthesis studies. This review examines the isolation and bioactivity of tryptophan-linked cyclic peptide natural products, along with a discussion of their first total synthesis, and biosynthesis where this has been studied.
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Affiliation(s)
- Jonathan A Swain
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand.
| | - Stephen R Walker
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand.
| | - Matthew B Calvert
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand.
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Symonds Street, Auckland 1010, New Zealand
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