1
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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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2
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Danelius E, Bu G, Wieske LHE, Gonen T. MicroED as a Powerful Tool for Structure Determination of Macrocyclic Drug Compounds Directly from Their Powder Formulations. ACS Chem Biol 2023; 18:2582-2589. [PMID: 37944119 PMCID: PMC10728894 DOI: 10.1021/acschembio.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as to act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally, and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles that have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material and that different conformations of flexible compounds can be derived from the same experiment. These results will have an impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- Emma Danelius
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Guanhong Bu
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Lianne H. E. Wieske
- Department
of Chemistry − BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - Tamir Gonen
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
- Department
of Physiology, University of California
Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
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3
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Yan LH, Li X, Wang BG. Natural products with 1,2-oxazine scaffold: occurrence, chemical diversity, bioactivity, synthesis, and biosynthesis. Nat Prod Rep 2023; 40:1874-1900. [PMID: 37642299 DOI: 10.1039/d3np00023k] [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: 08/31/2023]
Abstract
Covering: up to the end of July, 20231,2-Oxazine is a heterocyclic scaffold rarely found in natural products and is characterized by a directly connected N-O bond in a six-membered ring. Since the discovery of geneserine, the first 1,2-oxazine-containing natural product (1,2-oxazine NP) being isolated from Calabar bean (Physostigma venenosum) in 1925, a total of 76 naturally occurring 1,2-oxazine NPs have been isolated and identified from various sources, which have attracted the attention of researchers in the field of natural product chemistry, organic synthesis, biosynthesis, and pharmacology. This review summarizes the chemical family of 1,2-oxazine NPs, focusing on their source organisms, structural diversities, chemical synthesis, and biosynthesis.
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Affiliation(s)
- Li-Hong Yan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao 266237, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Xin Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Bin-Gui Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Wenhai Road 1, Qingdao 266237, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
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4
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Danelius E, Bu G, Wieske H, Gonen T. MicroED as a powerful tool for structure determination of macrocyclic drug compounds directly from their powder formulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551405. [PMID: 37577574 PMCID: PMC10418104 DOI: 10.1101/2023.07.31.551405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles which have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material, and that different conformations of flexible compounds can be derived from the same experiment. These results will have impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- E Danelius
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - G Bu
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - H Wieske
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - T Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
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5
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Yang Y, Kessler MGC, Marchán-Rivadeneira MR, Han Y. Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery. Molecules 2023; 28:molecules28104183. [PMID: 37241928 DOI: 10.3390/molecules28104183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.
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Affiliation(s)
- Yuehan Yang
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - Mara Grace C Kessler
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Honors Tutorial College, Ohio University, Athens, OH 45701, USA
| | - Maria Raquel Marchán-Rivadeneira
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
- Center for Research on Health in Latinamerica (CISeAL)-Biological Science Department, Pontificia Universidad Católica del Ecuador (PUCE), Quito 170143, Ecuador
| | - Yong Han
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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6
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Bitchagno GTM, Nchiozem-Ngnitedem VA, Melchert D, Fobofou SA. Demystifying racemic natural products in the homochiral world. Nat Rev Chem 2022; 6:806-822. [PMID: 37118098 PMCID: PMC9562063 DOI: 10.1038/s41570-022-00431-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 12/03/2022]
Abstract
Natural products possess structural complexity, diversity and chirality with attractive functions and biological activities that have significantly impacted drug discovery initiatives. Chiral natural products are abundant in nature but rarely occur as racemates. The occurrence of natural products as racemates is very intriguing from a biosynthetic point of view; as enzymes are chiral molecules, enzymatic reactions generating natural products should be stereospecific and lead to single-enantiomer products. Despite several reports in the literature describing racemic mixtures of stereoisomers isolated from natural sources, there has not been a comprehensive review of these intriguing racemic natural products. The discovery of many more natural racemates and their potential enzymatic sources in recent years allows us to describe the distribution and chemical diversity of this ‘class of natural products’ to enrich discussions on biosynthesis. In this Review, we describe the chemical classes, occurrence and distribution of pairs of enantiomers in nature and provide insights about recent advances in analytical methods used for their characterization. Special emphasis is on the biosynthesis, including plausible enzymatic and non-enzymatic formation of natural racemates, and their pharmacological significance. ![]()
Racemic natural products display a wealth of bioactivities and chemical diversity. Their derivation from intriguing racemization processes, through enzymatic or non-enzymatic pathways, are discussed here, as well as their pharmacological properties and the analytical techniques developed for their identification, resolution and characterization.
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7
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022; 61:e202202286. [PMID: 35384223 DOI: 10.1002/anie.202202286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 12/17/2022]
Abstract
Aromatic polyketides biosynthesized by microorganisms are a prominent class of natural products widely used in clinical treatments. Although genome mining approaches have accelerated the discovery of these molecules, the molecular diversity, abundance, and distribution of bacterial aromatic polyketides at a global scale remain elusive. Here, we provide a global atlas of bacterial aromatic polyketides based on large-scale analysis of type II polyketide synthases. We first established the chain length factor protein as a marker that can predict both chemical class and molecular uniqueness of the biosynthetic product, and analyzed the abundance, taxonomic distribution, estimated structural diversity, and the total number of aromatic polyketides in bacteria. We further show the identification of oryzanaphthopyrans with an unprecedented angular naphthopyran scaffold from a rare actinobacterium by genome mining guided by the global atlas. These results serve as a compass for exploiting the entire type II polyketide synthase-derived aromatic polyketides in bacteria.
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Affiliation(s)
- Shanchong Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang Province, 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
| | - Chi Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
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8
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shanchong Chen
- Zhejiang University Department of Chemistry Hangzhou CHINA
| | - Chi Zhang
- Westlake University School of Science Hangzhou CHINA
| | - Lihan Zhang
- Westlake University School of Science Shilongshan Rd.18Xihu District 310024 Hangzhou CHINA
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9
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Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022; 13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.
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Affiliation(s)
- F I Saldívar-González
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - V D Aldas-Bulos
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
| | - J L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - F Plisson
- CONACYT - Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
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10
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Park J, Li Y, Moon K, Han EJ, Lee SR, Seyedsayamdost MR. Structural Elucidation of Cryptic Algaecides in Marine Algal‐Bacterial Symbioses by NMR Spectroscopy and MicroED. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jong‐Duk Park
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Yuchen Li
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Kyuho Moon
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- College of Pharmacy Chonnam National University Gwangju 61186 South Korea
| | - Esther J. Han
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Seoung Rak Lee
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
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11
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Gorelik TE, Tehrani KHME, Gruene T, Monecke T, Niessing D, Kaiser U, Blankenfeldt W, Müller R. Crystal structure of natural product argyrin-D determined by 3D electron diffraction. CrystEngComm 2022. [DOI: 10.1039/d2ce00707j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structure of natural product argyrin D was determined from electron diffraction data.
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Affiliation(s)
- Tatiana E. Gorelik
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Kamaleddin H. M. E. Tehrani
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
| | - Tim Gruene
- Faculty of Chemistry, Department of Inorganic Chemistry, University of Vienna, AT-1090 Vienna, Austria
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Dierk Niessing
- Institute of Pharmaceutical Biotechnology, Ulm University, James-Franck-Ring N27, 89081 Ulm, Germany
| | - Ute Kaiser
- Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrucken, 66123, Germany
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12
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Hovestreydt E. Electron diffraction: Accelerating drug development. Drug Discov Today 2021; 27:371-373. [PMID: 34906690 DOI: 10.1016/j.drudis.2021.12.006] [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: 09/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/03/2022]
Abstract
Electron Diffraction (ED) is gaining momentum in science and industry. The application of ED for performing nanocrystallography is a disruptive innovation that is opening up fascinating new perspectives particularly for organic compounds required in the fields of chemical, pharmaceutical and advanced materials research.
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13
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Park JD, Li Y, Moon K, Han EJ, Lee SR, Seyedsayamdost MR. Structural Elucidation of Cryptic Algaecides in Marine Algal-Bacterial Symbioses by NMR Spectroscopy and MicroED. Angew Chem Int Ed Engl 2021; 61:e202114022. [PMID: 34852184 DOI: 10.1002/anie.202114022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Microbial secondary metabolite discovery is often conducted in pure monocultures. In a natural setting, however, where metabolites are constantly exchanged, biosynthetic precursors are likely provided by symbionts or hosts. In the current work, we report eight novel and architecturally unusual secondary metabolites synthesized by the bacterial symbiont Phaeobacter inhibens from precursors that, in a native context, would be provided by their algal hosts. Three of these were produced at low titres and their structures were determined de novo using the emerging microcrystal electron diffraction method. Some of the new metabolites exhibited potent algaecidal activity suggesting that the bacterial symbiont can convert algal precursors, tryptophan and sinapic acid, into complex cytotoxins. Our results have important implications for the parasitic phase of algal-bacterial symbiotic interactions.
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Affiliation(s)
- Jong-Duk Park
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Yuchen Li
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Kyuho Moon
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.,College of Pharmacy, Chonnam National University, Gwangju, 61186, South Korea
| | - Esther J Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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14
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Abstract
Introduction: Cannabis is a valuable plant, cultivated by humans for millennia. However, it has only been in the past several decades that biologists have begun to clarify the interesting Cannabis biosynthesis details, especially the production of its fascinating natural products termed acidic cannabinoids. Discussion: Acidic cannabinoids can experience a common organic chemistry reaction known as decarboxylation, transforming them into structural analogues referred to as neutral cannabinoids with far different pharmacology. This review addresses acidic and neutral cannabinoid structural pairs, when and where acidic cannabinoid decarboxylation occurs, the kinetics and mechanism of the decarboxylation reaction as well as possible future directions for this topic. Conclusions: Acidic cannabinoid decarboxylation is a unique transformation that has been increasingly investigated over the past several decades. Understanding how acidic cannabinoid decarboxylation occurs naturally as well as how it can be promoted or prevented during harvesting or storage is important for the various stakeholders in Cannabis cultivation.
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Affiliation(s)
- Crist N Filer
- PerkinElmer Health Sciences Inc., Waltham, Massachusetts, USA
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15
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Ghosh R, Bu G, Nannenga BL, Sumner LW. Recent Developments Toward Integrated Metabolomics Technologies (UHPLC-MS-SPE-NMR and MicroED) for Higher-Throughput Confident Metabolite Identifications. Front Mol Biosci 2021; 8:720955. [PMID: 34540897 PMCID: PMC8445028 DOI: 10.3389/fmolb.2021.720955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/17/2021] [Indexed: 02/03/2023] Open
Abstract
Metabolomics has emerged as a powerful discipline to study complex biological systems from a small molecule perspective. The success of metabolomics hinges upon reliable annotations of spectral features obtained from MS and/or NMR. In spite of tremendous progress with regards to analytical instrumentation and computational tools, < 20% of spectral features are confidently identified in most untargeted metabolomics experiments. This article explores the integration of multiple analytical instruments such as UHPLC-MS/MS-SPE-NMR and the cryo-EM method MicroED to achieve large-scale and confident metabolite identifications in a higher-throughput manner. UHPLC-MS/MS-SPE allows for the simultaneous automated purification of metabolites followed by offline structure elucidation and structure validation by NMR and MicroED. Large-scale study of complex metabolomes such as that of the model plant legume Medicago truncatula can be achieved using an integrated UHPLC-MS/MS-SPE-NMR metabolomics platform. Additionally, recent developments in MicroED to study structures of small organic molecules have enabled faster, easier and precise structure determinations of metabolites. A MicroED small molecule structure elucidation workflow (e.g., crystal screening, sample preparation, data collection and data processing/structure determination) has been described. Ongoing MicroED methods development and its future scope related to structure elucidation of specialized metabolites and metabolomics are highlighted. The incorporation of MicroED with a UHPLC-MS/MS-SPE-NMR instrumental ensemble offers the potential to accelerate and achieve higher rates of metabolite identification.
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Affiliation(s)
- Rajarshi Ghosh
- Division of Biochemistry, University of Missouri, Columbia, MO, United States
- MU Metabolomics Center, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, SC, United States
- Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
| | - Guanhong Bu
- Chemical Engineering, School for Engineering of Matter, Transport & Energy, Arizona State University, Tempe, AZ, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport & Energy, Arizona State University, Tempe, AZ, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lloyd W. Sumner
- Division of Biochemistry, University of Missouri, Columbia, MO, United States
- MU Metabolomics Center, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, SC, United States
- Interdisciplinary Plant Group, University of Missouri, Columbia, SC, United States
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16
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Medema MH, de Rond T, Moore BS. Mining genomes to illuminate the specialized chemistry of life. Nat Rev Genet 2021; 22:553-571. [PMID: 34083778 PMCID: PMC8364890 DOI: 10.1038/s41576-021-00363-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
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Affiliation(s)
- Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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17
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Hall CL, Andrusenko I, Potticary J, Gao S, Liu X, Schmidt W, Marom N, Mugnaioli E, Gemmi M, Hall SR. 3D Electron Diffraction Structure Determination of Terrylene, a Promising Candidate for Intermolecular Singlet Fission. Chemphyschem 2021; 22:1631-1637. [PMID: 34117821 PMCID: PMC8457070 DOI: 10.1002/cphc.202100320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/05/2021] [Indexed: 12/13/2022]
Abstract
Herein we demonstrate the prowess of the 3D electron diffraction approach by unveiling the structure of terrylene, the third member in the series of peri‐condensed naphthalene analogues, which has eluded structure determination for 65 years. The structure was determined by direct methods using electron diffraction data and corroborated by dispersion‐inclusive density functional theory optimizations. Terrylene crystalizes in the monoclinic space group P21/a, arranging in a sandwich‐herringbone packing motif, similar to analogous compounds. Having solved the crystal structure, we use many‐body perturbation theory to evaluate the excited‐state properties of terrylene in the solid‐state. We find that terrylene is a promising candidate for intermolecular singlet fission, comparable to tetracene and rubrene.
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Affiliation(s)
- Charlie L Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Iryna Andrusenko
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Siyu Gao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xingyu Liu
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Enrico Mugnaioli
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Mauro Gemmi
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Simon R Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
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18
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Gruene T, Holstein JJ, Clever GH, Keppler B. Establishing electron diffraction in chemical crystallography. Nat Rev Chem 2021; 5:660-668. [PMID: 37118416 DOI: 10.1038/s41570-021-00302-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The emerging field of 3D electron diffraction (3D ED) opens new opportunities for structure determination from sub-micrometre-sized crystals. Although the foundations of this technology emerged earlier, the past decade has seen developments in cryo-electron microscopy and (X-ray) crystallography that particularly enable the widespread use of 3D ED. This Perspective describes to chemists and chemical crystallographers just how similar electron and X-ray diffraction are and discusses their complementary aspects. We wish to establish 3D ED in the broader chemistry community, such that electron crystallography becomes a common part of the analytical chemistry toolkit. With a suitable instrument at their disposal, every skilled crystallographer can quickly learn to perform structure determinations using 3D ED.
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19
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Sekharan S, Liu X, Yang Z, Liu X, Deng L, Ruan S, Abramov Y, Sun G, Li S, Zhou T, Shi B, Zeng Q, Zeng Q, Chang C, Jin Y, Shi X. Selecting a stable solid form of remdesivir using microcrystal electron diffraction and crystal structure prediction. RSC Adv 2021; 11:17408-17412. [PMID: 35479679 PMCID: PMC9033196 DOI: 10.1039/d1ra03100g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/20/2022] Open
Abstract
Therapeutic options in response to the coronavirus disease 2019 (COVID-19) outbreak are urgently needed. In this communication, we demonstrate how to support selection of a stable solid form of an antiviral drug remdesivir in quick time using the microcrystal electron diffraction (MicroED) technique and a cloud-based and artificial intelligence implemented crystal structure prediction platform. We present the MicroED structures of remdesivir forms II and IV and conclude that form II is more stable than form IV at ambient temperature in agreement with experimental observations. The combined experimental and theoretical study can serve as a template for formulation scientists in the pharmaceutical industry.
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Affiliation(s)
| | - Xuetao Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Zhuocen Yang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xiang Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Li Deng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Shigang Ruan
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yuriy Abramov
- XtalPi Inc. 245 Main St, Floor 11 Cambridge MA 02142 USA
| | - GuangXu Sun
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Sizhu Li
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Tian Zhou
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Baime Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qun Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qiao Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Chao Chang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yingdi Jin
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xuekun Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
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20
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Figueiredo SAC, Preto M, Moreira G, Martins TP, Abt K, Melo A, Vasconcelos VM, Leão PN. Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues*. Angew Chem Int Ed Engl 2021; 60:10064-10072. [PMID: 33599093 PMCID: PMC8252387 DOI: 10.1002/anie.202015105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Indexed: 12/16/2022]
Abstract
In recent years, extensive sequencing and annotation of bacterial genomes has revealed an unexpectedly large number of secondary metabolite biosynthetic gene clusters whose products are yet to be discovered. For example, cyanobacterial genomes contain a variety of gene clusters that likely incorporate fatty acid derived moieties, but for most cases we lack the knowledge and tools to effectively predict or detect the encoded natural products. Here, we exploit the apparent absence of a functional β-oxidation pathway in cyanobacteria to achieve efficient stable-isotope-labeling of their fatty acid derived lipidome. We show that supplementation of cyanobacterial cultures with deuterated fatty acids can be used to easily detect natural product signatures in individual strains. The utility of this strategy is demonstrated in two cultured cyanobacteria by uncovering analogues of the multidrug-resistance reverting hapalosin, and novel, cytotoxic, lactylate-nocuolin A hybrids-the nocuolactylates.
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Affiliation(s)
- Sandra A. C. Figueiredo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Marco Preto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Gabriela Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
| | - Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)University of PortoRua de Jorge Viterbo Ferreira, 2284050-313PortoPortugal
| | - Kathleen Abt
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)University of PortoRua de Jorge Viterbo Ferreira, 2284050-313PortoPortugal
| | - André Melo
- LAQV@REQUIMTE/Department of Chemistry and BiochemistryFaculty of SciencesUniversity of PortoRua do Campo Alegre4169-007PortoPortugal
| | - Vitor M. Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
- Department of BiologyFaculty of SciencesUniversity of PortoRua do Campo Alegre4169-007PortoPortugal
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR)University of PortoAvenida General Norton de Matos, s/n4450-208MatosinhosPortugal
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21
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Cardenal A, Ramadhar TR. Application of Crystalline Matrices for the Structural Determination of Organic Molecules. ACS CENTRAL SCIENCE 2021; 7:406-414. [PMID: 33791424 PMCID: PMC8006175 DOI: 10.1021/acscentsci.0c01492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 06/12/2023]
Abstract
While single-crystal X-ray diffraction (SC-XRD) is one of the most powerful structural determination techniques for organic molecules, the requirement of obtaining a suitable crystal for analysis limits its applicability, particularly for liquids and amorphous solids. The emergent use of preformed porous crystalline matrices that can absorb organic compounds and stabilize them via host-guest interactions for observation via SC-XRD offers a way to overcome this hindrance. A topical and current discussion of SC-XRD in organic chemistry and the use of preformed matrices for the in crystallo analysis of organic compounds, with a particular focus on the absolute structure determination of chiral molecules, is presented. Preformed crystalline matrices that are covered include metal-organic frameworks (MOFs) as used in the crystalline sponge method, metal-organic polyhedra (MOPs, coordination cages), porous organic materials (POMs)/porous organic molecular crystals (POMCs), and biological scaffolds. An outlook and perspective on the current technology and on its future directions is provided.
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Affiliation(s)
- Ashley
D. Cardenal
- Department of Chemistry, Howard University, Washington, DC 20059, United States
| | - Timothy R. Ramadhar
- Department of Chemistry, Howard University, Washington, DC 20059, United States
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22
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Ueda M, Aoki T, Akiyama T, Nakamuro T, Yamashita K, Yanagisawa H, Nureki O, Kikkawa M, Nakamura E, Aida T, Itoh Y. Alternating Heterochiral Supramolecular Copolymerization. J Am Chem Soc 2021; 143:5121-5126. [DOI: 10.1021/jacs.1c00823] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Michihisa Ueda
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsubasa Aoki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takayoshi Akiyama
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | | | | | | | | | | | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshimitsu Itoh
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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23
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Crüsemann M. Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows. Mar Drugs 2021; 19:142. [PMID: 33807702 PMCID: PMC7998270 DOI: 10.3390/md19030142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/18/2022] Open
Abstract
Bacterial natural products possess potent bioactivities and high structural diversity and are typically encoded in biosynthetic gene clusters. Traditional natural product discovery approaches rely on UV- and bioassay-guided fractionation and are limited in terms of dereplication. Recent advances in mass spectrometry, sequencing and bioinformatics have led to large-scale accumulation of genomic and mass spectral data that is increasingly used for signature-based or correlation-based mass spectrometry genome mining approaches that enable rapid linking of metabolomic and genomic information to accelerate and rationalize natural product discovery. In this mini-review, these approaches are presented, and discovery examples provided. Finally, future opportunities and challenges for paired omics-based natural products discovery workflows are discussed.
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Affiliation(s)
- Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
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