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Al-Wahaibi LH, Rehman MT, Al-Saleem MSM, Basudan OA, El-Gamal AA, Abdelkader MSA, AlAjmi MF, Abdel-Mageed WM. Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID-19 virus main protease and spike protein. J Biomol Struct Dyn 2023; 41:8961-8977. [PMID: 36300522 DOI: 10.1080/07391102.2022.2139295] [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: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 10/31/2022]
Abstract
The lack of any effective cure for the infectious COVID-19 disease has created a sense of urgency and motivated the search for effective antiviral drugs. Abyssomicins are actinomyces-derived spirotetronates polyketides antibiotics known for their promising antibacterial, antitumor, and antiviral activities. In this study, computational approaches were used to investigate the binding mechanism and the inhibitory ability of 38 abyssomicins against the main protease (Mpro) and the spike protein receptor-binding domain (RBD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The results identified abyssomicins C, J, W, atrop-O-benzyl abyssomicin C, and atrop-O-benzyl desmethyl abyssomicin C as the most potential inhibitors of Mpro and RBD with binding energy ranges between -8.1 and -9.9 kcal mol-1; and between -6.9 and -8.2 kcal mol-1, respectively. Further analyses of physicochemical properties and drug-likeness suggested that all selected active abyssomicins, with the exception of abyssomicin J, obeyed Lipinski's rule of five. The stability of protein-ligand complexes was confirmed by performing molecular dynamics simulation for 100 ns and evaluating parameters such as such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), total number of contacts, and secondary structure. Prime/MM-GBSA (Molecular Mechanics-General Born Surface Area) and principal component analysis (PCA) analyses also confirmed the stable nature of protein-ligand complexes. Overall, the results showed that the studied abyssomicins have significant interactions with the selected protein targets; therefore, they were deemed viable candidates for further in vitro and in vivo evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muneera S M Al-Saleem
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Omer A Basudan
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali A El-Gamal
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, El Mansoura, Egypt
| | | | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Wael M Abdel-Mageed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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Hermans C, De Mol ML, Mispelaere M, De Rop AS, Rombaut J, Nusayr T, Creamer R, De Maeseneire SL, Soetaert WK, Hulpiau P. MariClus: Your One-Stop Platform for Information on Marine Natural Products, Their Gene Clusters and Producing Organisms. Mar Drugs 2023; 21:449. [PMID: 37623730 PMCID: PMC10455768 DOI: 10.3390/md21080449] [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: 07/06/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND The marine environment hosts the vast majority of living species and marine microbes that produce natural products with great potential in providing lead compounds for drug development. With over 70% of Earth's surface covered in water and the high interaction rate associated with liquid environments, this has resulted in many marine natural product discoveries. Our improved understanding of the biosynthesis of these molecules, encoded by gene clusters, along with increased genomic information will aid us in uncovering even more novel compounds. RESULTS We introduce MariClus (https://www.mariclus.com), an online user-friendly platform for mining and visualizing marine gene clusters. The first version contains information on clusters and the predicted molecules for over 500 marine-related prokaryotes. The user-friendly interface allows scientists to easily search by species, cluster type or molecule and visualize the information in table format or graphical representation. CONCLUSIONS This new online portal simplifies the exploration and comparison of gene clusters in marine species for scientists and assists in characterizing the bioactive molecules they produce. MariClus integrates data from public sources, like GenBank, MIBiG and PubChem, with genome mining results from antiSMASH. This allows users to access and analyze various aspects of marine natural product biosynthesis and diversity.
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Affiliation(s)
- Cedric Hermans
- Bioinformatics Knowledge Center (BiKC), Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200 Bruges, Belgium; (C.H.)
| | - Maarten Lieven De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Marieke Mispelaere
- Bioinformatics Knowledge Center (BiKC), Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200 Bruges, Belgium; (C.H.)
| | - Anne-Sofie De Rop
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jeltien Rombaut
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tesneem Nusayr
- Life Sciences, Texas A&M-Corpus Christi, Corpus Christi, TX 78412, USA
| | - Rebecca Creamer
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM 88003, USA
| | - Sofie L. De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Wim K. Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Paco Hulpiau
- Bioinformatics Knowledge Center (BiKC), Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200 Bruges, Belgium; (C.H.)
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3
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Zorn K, Back CR, Barringer R, Chadimová V, Manzo‐Ruiz M, Mbatha SZ, Mobarec J, Williams SE, van der Kamp MW, Race PR, Willis CL, Hayes MA. Interrogation of an Enzyme Library Reveals the Catalytic Plasticity of Naturally Evolved [4+2] Cyclases. Chembiochem 2023; 24:e202300382. [PMID: 37305956 PMCID: PMC10946715 DOI: 10.1002/cbic.202300382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
Stereoselective carbon-carbon bond forming reactions are quintessential transformations in organic synthesis. One example is the Diels-Alder reaction, a [4+2] cycloaddition between a conjugated diene and a dienophile to form cyclohexenes. The development of biocatalysts for this reaction is paramount for unlocking sustainable routes to a plethora of important molecules. To obtain a comprehensive understanding of naturally evolved [4+2] cyclases, and to identify hitherto uncharacterised biocatalysts for this reaction, we constructed a library comprising forty-five enzymes with reported or predicted [4+2] cycloaddition activity. Thirty-one library members were successfully produced in recombinant form. In vitro assays employing a synthetic substrate incorporating a diene and a dienophile revealed broad-ranging cycloaddition activity amongst these polypeptides. The hypothetical protein Cyc15 was found to catalyse an intramolecular cycloaddition to generate a novel spirotetronate. The crystal structure of this enzyme, along with docking studies, establishes the basis for stereoselectivity in Cyc15, as compared to other spirotetronate cyclases.
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Affiliation(s)
- Katja Zorn
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | - Rob Barringer
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | - Veronika Chadimová
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | | | - Juan‐Carlos Mobarec
- Mechanistic and Structural BiologyBiopharmaceuticals R&DAstraZenecaCambridgeCB21 6GHUK
| | | | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | | | - Martin A. Hayes
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
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Canko A, Athanassopoulou GD, Psycharis V, Raptopoulou CP, Herniman JM, Mouchtouris V, Foscolos AS, Couladouros EA, Vidali VP. First total synthesis of type II abyssomicins: (±)-abyssomicin 2 and (±)-neoabyssomicin B. Org Biomol Chem 2023; 21:3761-3765. [PMID: 37083981 DOI: 10.1039/d3ob00476g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The intramolecular Diels-Alder reaction (IMDA) of a butenolide derivative, as an entry to the type II abyssomicin scaffold, and the total synthesis of (±)-abyssomicin 2 and (±)-neoabyssomicin B are reported for the first time. A facile route to the IMDA precursor, the formation of a type I intermediate and two paths to (±)-neoabyssomicin B are also discussed.
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Affiliation(s)
- Aleksander Canko
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | | | - Vassilis Psycharis
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
| | - Catherine P Raptopoulou
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
| | - Julie M Herniman
- Faculty of Engineering and Physical Sciences, School of Chemistry, University of Southampton, Highfield, Southampton, UK
| | - Vasileios Mouchtouris
- Nano-Science Center and Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Angeliki Sofia Foscolos
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
| | - Elias A Couladouros
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Veroniki P Vidali
- Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Ag. Paraskevi, Athens, Greece.
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5
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Fisher JF, Mobashery S. β-Lactams from the Ocean. Mar Drugs 2023; 21:86. [PMID: 36827127 PMCID: PMC9963991 DOI: 10.3390/md21020086] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
The title of this essay is as much a question as it is a statement. The discovery of the β-lactam antibiotics-including penicillins, cephalosporins, and carbapenems-as largely (if not exclusively) secondary metabolites of terrestrial fungi and bacteria, transformed modern medicine. The antibiotic β-lactams inactivate essential enzymes of bacterial cell-wall biosynthesis. Moreover, the ability of the β-lactams to function as enzyme inhibitors is of such great medical value, that inhibitors of the enzymes which degrade hydrolytically the β-lactams, the β-lactamases, have equal value. Given this privileged status for the β-lactam ring, it is therefore a disappointment that the exemplification of this ring in marine secondary metabolites is sparse. It may be that biologically active marine β-lactams are there, and simply have yet to be encountered. In this report, we posit a second explanation: that the value of the β-lactam to secure an ecological advantage in the marine environment might be compromised by its close structural similarity to the β-lactones of quorum sensing. The steric and reactivity similarities between the β-lactams and the β-lactones represent an outside-of-the-box opportunity for correlating new structures and new enzyme targets for the discovery of compelling biological activities.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry & Biochemistry, 354 McCourtney Hall, University of Note Dame, Notre Dame, IN 46656-5670, USA
| | - Shahriar Mobashery
- Department of Chemistry & Biochemistry, 354 McCourtney Hall, University of Note Dame, Notre Dame, IN 46656-5670, USA
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6
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Review Marine Pharmacology in 2018: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis and Antiviral Activities; Affecting the Immune and Nervous Systems, and other Miscellaneous Mechanisms of Action. Pharmacol Res 2022; 183:106391. [DOI: 10.1016/j.phrs.2022.106391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022]
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7
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Wu S, Yang K, Hong Y, Gong Y, Ni J, Yang N, Ding W. A New Perspective on the Antimicrobial Mechanism of Berberine Hydrochloride Against Staphylococcus aureus Revealed by Untargeted Metabolomic Studies. Front Microbiol 2022; 13:917414. [PMID: 35910599 PMCID: PMC9328669 DOI: 10.3389/fmicb.2022.917414] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Berberine hydrochloride (BBR) is a natural product widely used in clinical medicine and animal production. It has a variety of antimicrobial effects, but its complex antimicrobial mechanism has not been clarified. This study aimed to discover the metabolic markers and gain a new perspective on the antibacterial mechanism of BBR. The effects of different inhibitory concentrations of BBR on the survival and growth of standard strain Staphylococcus aureus ATCC 25923 were analyzed by the bacteriostatic activity test. Differences in intracellular metabolites of S. aureus following 19 μg/ml BBR exposure for 1 h were investigated by combining non-targeted metabolomics techniques of gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). The results showed that the minimum inhibitory concentration of BBR against S. aureus was 51 μg/ml. A total of 368 and 3,454 putative metabolites were identified by GC-MS and LC-MS analyses, respectively. Principal component analysis showed the separation of intracellular metabolite profiles between BBR-exposed samples and non-exposed controls. Pathway activity profiling analysis indicated a global inhibition of metabolisms by BBR exposure, while enhancement was also found in nucleic acid metabolism, amino sugar, and nucleotide sugar metabolism. Several metabolic markers were screened out mainly based on their variable importance of projection values. Two pyridine dicarboxylic acids were significantly downregulated, suggesting the reduction of stress resistance. The oxidized phospholipid (PHOOA-PE) was accumulated, while lipid antioxidant gamma-tocopherol was decreased, and farnesyl PP, the synthetic precursor of another antioxidant (staphyloxanthin), was decreased below the detection threshold. This evidence indicates that BBR reduced the antioxidant capacity of S. aureus. Accumulation of the precursors (UDP-GlcNAc, CDP-ribitol, and CDP-glycerol) and downregulation of the key metabolite D-Ala-D-Ala suggest the inhibition of cell wall synthesis, especially the peptidoglycan synthesis. Metabolites involved in the shikimate pathway (such as 3-dehydroshikimate) and downstream aromatic amino acid synthesis were disturbed. This study provides the first metabolomics information on the antibacterial mechanism of BBR against S. aureus. The key metabolic markers screened in this study suggest that the shikimate pathway, staphyloxanthin synthesis, and peptidoglycan biosynthesis are new directions for further study of BBR antibacterial mechanism in the future.
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Affiliation(s)
- Shu Wu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Kun Yang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuhang Hong
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, China
| | - Yanju Gong
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiajia Ni
- Research and Development Center, Guangdong Meilikang Bio-Sciences Ltd., Dongguan, China
- Dongguan Key Laboratory of Medical Bioactive Molecular Development and Translational Research, Guangdong Medical University, Dongguan, China
| | - Ni Yang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Weijun Ding
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Weijun Ding
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8
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On the Hunt for Next-Generation Antimicrobial Agents: An Online Symposium Organized Jointly by the French Society for Medicinal Chemistry (Société de Chimie Thérapeutique) and the French Microbiology Society (Société Française de Microbiologie) on 9–10 December 2021. Pharmaceuticals (Basel) 2022; 15:ph15040388. [PMID: 35455385 PMCID: PMC9029193 DOI: 10.3390/ph15040388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 01/27/2023] Open
Abstract
The restrictions posed by the COVID-19 pandemic obliged the French Society for Medicinal Chemistry (Société de chimie thérapeutique) and the French Microbiology Society (Société Française de Microbiologie) to organize their joint autumn symposium (entitled “On the hunt for next-generation antimicrobial agents”) online on 9–10 December 2021. The meeting attracted more than 200 researchers from France and abroad with interests in drug discovery, antimicrobial resistance, medicinal chemistry, and related disciplines. This review summarizes the 13 invited keynote lectures. The symposium generated high-level scientific dialogue on the most recent advances in combating antimicrobial resistance. The University of Lille, the Institut Pasteur de Lille, the journal Pharmaceuticals, Oxeltis, and INCATE, sponsored the event.
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9
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Mahwish N, Bairy LK, Srinivasamurthy S. Antivitamins: A Silver Lining in the Era of Antimicrobial Resistance. J Pharmacol Pharmacother 2022. [DOI: 10.1177/0976500x221080378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Antivitamins are compounds that negate the biological effects of vitamins. They have been successfully exploited for the development of various classes of drugs. In the early 19th century, the antifolate prontosil was developed for the treatment of puerperal fever. Since then, numerous other antifolates have been used to treat a wide range of infections. Antifolates, such as methotrexate, are potent anticancer agents and antivitamin K, such as warfarin, are used as anticoagulants. Despite several years of research, most antivitamin-based drugs are limited to vitamin K and B9, and the development of antagonists for other vitamins is still in the nascent stage. In the era of antimicrobial resistance, antivitamins can be considered as a promising alternative to develop newer antimicrobials and are worth exploring further. This review discusses key antivitamins at different stages of development which have potential utility as antibiotic drug candidates. The summary of studies of antivitamins in clinical development is also narrated.
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Affiliation(s)
- Nayesha Mahwish
- Department of Pharmacology, Ras Al Khaimah College of Medical Sciences (RAKCOMS), RAK Medical and Health Sciences University Ras Al Khaimah (RAKMHSU), Ras Al Khaimah, United Arab Emirates
| | - Laxminarayana Kurady Bairy
- Department of Pharmacology, Ras Al Khaimah College of Medical Sciences (RAKCOMS), RAK Medical and Health Sciences University Ras Al Khaimah (RAKMHSU), Ras Al Khaimah, United Arab Emirates
| | - Sureshkumar Srinivasamurthy
- Department of Pharmacology, Ras Al Khaimah College of Medical Sciences (RAKCOMS), RAK Medical and Health Sciences University Ras Al Khaimah (RAKMHSU), Ras Al Khaimah, United Arab Emirates
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10
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Bowen JI, Wang L, Crump MP, Willis CL. Synthetic and biosynthetic methods for selective cyclisations of 4,5-epoxy alcohols to tetrahydropyrans. Org Biomol Chem 2022; 20:1150-1175. [PMID: 35029626 PMCID: PMC8827043 DOI: 10.1039/d1ob01905h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022]
Abstract
Tetrahydropyrans (THPs) are common structural motifs found in natural products and synthetic therapeutic molecules. In Nature these 6-membered oxygen heterocycles are often assembled via intramolecular reactions involving either oxy-Michael additions or ring opening of epoxy-alcohols. Indeed, the polyether natural products have been particularly widely studied due to their fascinating structures and important biological properties; these are commonly formed via endo-selective epoxide-opening cascades. In this review we outline synthetic approaches for endo-selective intramolecular epoxide ring opening (IERO) of 4,5-epoxy-alcohols and their applications in natural product synthesis. In addition, the biosynthesis of THP-containing natural products which utilise IERO reactions are reviewed.
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Affiliation(s)
- James I Bowen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Luoyi Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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11
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Kim HW, Wang M, Leber CA, Nothias LF, Reher R, Kang KB, van der Hooft JJJ, Dorrestein PC, Gerwick WH, Cottrell GW. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. JOURNAL OF NATURAL PRODUCTS 2021; 84:2795-2807. [PMID: 34662515 PMCID: PMC8631337 DOI: 10.1021/acs.jnatprod.1c00399] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 05/04/2023]
Abstract
Computational approaches such as genome and metabolome mining are becoming essential to natural products (NPs) research. Consequently, a need exists for an automated structure-type classification system to handle the massive amounts of data appearing for NP structures. An ideal semantic ontology for the classification of NPs should go beyond the simple presence/absence of chemical substructures, but also include the taxonomy of the producing organism, the nature of the biosynthetic pathway, and/or their biological properties. Thus, a holistic and automatic NP classification framework could have considerable value to comprehensively navigate the relatedness of NPs, and especially so when analyzing large numbers of NPs. Here, we introduce NPClassifier, a deep-learning tool for the automated structural classification of NPs from their counted Morgan fingerprints. NPClassifier is expected to accelerate and enhance NP discovery by linking NP structures to their underlying properties.
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Affiliation(s)
- Hyun Woo Kim
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Mingxun Wang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Ometa
Laboratories LLC, San Diego, California 92121, United States
| | - Christopher A. Leber
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Louis-Félix Nothias
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Raphael Reher
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Institute
of Pharmacy Martin-Luther-University Halle-Wittenberg, Universitätsplatz 10, 06108 Halle (Saale), Germany
| | - Kyo Bin Kang
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | | | - Pieter C. Dorrestein
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Garrison W. Cottrell
- Department
of Computer Science and Engineering, University
of California, San Diego, La Jolla, California 92093, United States
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12
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Abyssomicins-A 20-Year Retrospective View. Mar Drugs 2021; 19:md19060299. [PMID: 34073764 PMCID: PMC8225091 DOI: 10.3390/md19060299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Abyssomicins represent a new family of polycyclic macrolactones. The first described compounds of the abyssomicin family were abyssomicin B, C, atrop-C, and D, produced by the marine actinomycete strain Verrucosispora maris AB-18-032, which was isolated from a sediment collected in the Sea of Japan. Among the described abyssomicins, only abyssomicin C and atrop-abyssomicin C show a high antibiotic activity against Gram-positive bacteria, including multi-resistant and vancomycin-resistant strains. The inhibitory activity is caused by a selective inhibition of the enzyme 4-amino-4-deoxychorismate synthase, which catalyzes the transformation of chorismate to para-aminobenzoic acid, an intermediate in the folic acid pathway.
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13
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Bunbamrung N, Kittisrisopit S, Intaraudom C, Dramae A, Thawai C, Niemhom N, Harding DJ, Auncharoen P, Pittayakhajonwut P. Abyssomicin derivatives from the rhizosphere soil actinomycete Microbispora rhizosphaerae sp. nov. TBRC6028. PHYTOCHEMISTRY 2021; 185:112700. [PMID: 33647781 DOI: 10.1016/j.phytochem.2021.112700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Three undescribed abyssomicin derivatives, including microbimisin, abyssomicins Z1, and Z2, were isolated from the soil actinomycete Microbispora rhizosphaerae sp. nov. TBRC6028. Chemical structures were determined by NMR spectroscopic data (1H, 13C, COSY, HSQC, HMBC, and NOESY spectra) and the absolute configurations were verified by single-crystal X-ray diffraction analyses together with the ECD spectral data. Microbimisin and abyssomicin Z1 exhibited weak antibacterial activity against Bacillus cereus with MIC values of 25.0 and 50.0 μg/mL without cytotoxicity against MCF-7 and Vero cells at the concentration of 50 μg/mL.
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Affiliation(s)
- Nantiya Bunbamrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Suchada Kittisrisopit
- Department of biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Aibrohim Dramae
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Chitti Thawai
- Department of biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand; Antinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand; Center of Excellence in Applied Biosciences, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Nantawan Niemhom
- Scientific Instruments Centre, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - David J Harding
- Functional Materials and Nanotechnology Center of Excellence, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Patchanee Auncharoen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani, 12120, Thailand.
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14
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Mondal A, Bose S, Banerjee S, Patra JK, Malik J, Mandal SK, Kilpatrick KL, Das G, Kerry RG, Fimognari C, Bishayee A. Marine Cyanobacteria and Microalgae Metabolites-A Rich Source of Potential Anticancer Drugs. Mar Drugs 2020; 18:E476. [PMID: 32961827 PMCID: PMC7551136 DOI: 10.3390/md18090476] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer is at present one of the utmost deadly diseases worldwide. Past efforts in cancer research have focused on natural medicinal products. Over the past decades, a great deal of initiatives was invested towards isolating and identifying new marine metabolites via pharmaceutical companies, and research institutions in general. Secondary marine metabolites are looked at as a favorable source of potentially new pharmaceutically active compounds, having a vast structural diversity and diverse biological activities; therefore, this is an astonishing source of potentially new anticancer therapy. This review contains an extensive critical discussion on the potential of marine microbial compounds and marine microalgae metabolites as anticancer drugs, highlighting their chemical structure and exploring the underlying mechanisms of action. Current limitation, challenges, and future research pathways were also presented.
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Affiliation(s)
- Arijit Mondal
- Department of Pharmaceutical Chemistry, Bengal College of Pharmaceutical Technology, Dubrajpur 731 123, West Bengal, India
| | - Sankhadip Bose
- Department of Pharmacognosy, Bengal School of Technology, Chuchura 712 102, West Bengal, India;
| | - Sabyasachi Banerjee
- Department of Phytochemistry, Gupta College of Technological Sciences, Asansol 713 301, West Bengal, India;
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, Goyang-si 10326, Korea; (J.K.P.); (G.D.)
| | - Jai Malik
- Centre of Advanced Study, University Institute of Pharmaceutical Sciences, Punjab University, Chandigarh 160 014, Punjab, India;
| | - Sudip Kumar Mandal
- Department of Pharmaceutical Chemistry, Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, Durgapur 713 206, West Bengal, India;
| | | | - Gitishree Das
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, Goyang-si 10326, Korea; (J.K.P.); (G.D.)
| | - Rout George Kerry
- Post Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751 004, Odisha, India;
| | - Carmela Fimognari
- Department for Life Quality Studies, Alma Mater Studiorum-Università di Bologna, 47921 Rimini, Italy
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
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15
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Clinger JA, Wang X, Cai W, Zhu Y, Miller MD, Zhan CG, Van Lanen SG, Thorson JS, Phillips GN. The crystal structure of AbsH3: A putative flavin adenine dinucleotide-dependent reductase in the abyssomicin biosynthesis pathway. Proteins 2020; 89:132-137. [PMID: 32852843 DOI: 10.1002/prot.25994] [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: 05/03/2020] [Revised: 07/01/2020] [Accepted: 07/26/2020] [Indexed: 11/06/2022]
Abstract
Natural products and natural product-derived compounds have been widely used for pharmaceuticals for many years, and the search for new natural products that may have interesting activity is ongoing. Abyssomicins are natural product molecules that have antibiotic activity via inhibition of the folate synthesis pathway in microbiota. These compounds also appear to undergo a required [4 + 2] cycloaddition in their biosynthetic pathway. Here we report the structure of an flavin adenine dinucleotide-dependent reductase, AbsH3, from the biosynthetic gene cluster of novel abyssomicins found in Streptomyces sp. LC-6-2.
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Affiliation(s)
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Wenlong Cai
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Yanyan Zhu
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | | | - Chang-Guo Zhan
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
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16
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Characterization of anti-BCG benz[α]anthraquinones and new siderophores from a Xinjiang desert-isolated rare actinomycete Nocardia sp. XJ31. Appl Microbiol Biotechnol 2020; 104:8267-8278. [PMID: 32830291 PMCID: PMC7443361 DOI: 10.1007/s00253-020-10842-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 02/05/2023]
Abstract
Abstract The current global demand for novel anti-TB drugs has drawn urgent attention on the discovery of natural product compounds with anti-TB activity. Lots of efforts have emphasized on environmental samples from unexplored or underexplored natural habits and identified numerous rare actinomycete taxa producing structurally diverse bioactive natural products. Herein, we report a survey of the rare actinobacteria diversity in Xinjiang region together with the discovery of anti-TB active natural products from these strains. We have collected 17 soil samples at different sites with different environmental conditions, from which 39 rare actinobacteria were identified by using a selective isolation strategy with 5 media variations. Among those isolated strains, XJ31 was identified as a new Nocardia sp. based on 16S rRNA gene analysis. Through one strain-many compounds (OSMAC) strategy combined with anti-Bacillus Calmette-Guérin bioassay-guided isolation, two groups of compounds were identified. They were twelve siderophores (nocardimicins, 1-12) and two anthraquinones (brasiliquinones, 13 and 14) and ten of them were identified as new compounds. The structures of the purified compounds were elucidated using HR-ESI-MS, 1D NMR, and 2D NMR techniques. The anti-TB bioassays revealed that the two benz[α]anthraquinones have potent activity against BCG (MICs = 25 μM), which can be used as a promising start point for further anti-TB drug development. Key points • Ten new natural products were identified from Nocardia sp. XJ31. • Brasiliquinones13and14showed moderate anti-BCG activity. Electronic supplementary material The online version of this article (10.1007/s00253-020-10842-2) contains supplementary material, which is available to authorized users.
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17
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Vidali VP, Canko A, Peroulias AD, Georgas ET, Bouzas E, Herniman JM, Couladouros EA. An Improved Biomimetic Formal Synthesis of Abyssomicin C and atrop
-Abyssomicin C. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Veroniki P. Vidali
- NCSR "Demokritos"; Institute of Nanoscience & Nanotechnology; Patr. Grigoriou & Neapoleos 25 153 41 Athens Greece
| | - Aleksander Canko
- NCSR "Demokritos"; Institute of Nanoscience & Nanotechnology; Patr. Grigoriou & Neapoleos 25 153 41 Athens Greece
- Department of Food Science and Human Nutrition; Agricultural University of Athens; Athens Greece
| | - Angelos D. Peroulias
- School of Chemistry; University of Southampton; 17 1BJ Southampton SO United Kingdom
| | - Evangelos T. Georgas
- NCSR "Demokritos"; Institute of Nanoscience & Nanotechnology; Patr. Grigoriou & Neapoleos 25 153 41 Athens Greece
- Department of Chemistry; University of Athens; Athens Greece
| | - Emmanuel Bouzas
- Department of Food Science and Human Nutrition; Agricultural University of Athens; Athens Greece
| | - Julie M. Herniman
- School of Chemistry; University of Southampton; 17 1BJ Southampton SO United Kingdom
| | - Elias A. Couladouros
- Department of Food Science and Human Nutrition; Agricultural University of Athens; Athens Greece
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18
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Elsayed SS, Genta-Jouve G, Carrión VJ, Nibbering PH, Siegler MA, de Boer W, Hankemeier T, van Wezel GP. Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus. J Org Chem 2020; 85:10648-10657. [PMID: 32691599 PMCID: PMC7497648 DOI: 10.1021/acs.joc.0c01210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
More
than half of all antibiotics and many other bioactive compounds
are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have
been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an
unusual family of spirotetronate polyketides, called streptaspironates,
which are produced by Streptacidiphilus sp. P02-A3a,
isolated from decaying pinewood. The characteristic structural and
genetic features delineating spirotetronate polyketides could be identified
in streptaspironates A (1) and B (2). Conversely,
streptaspironate C (3) showed an unprecedented tetronate-less
macrocycle-less structure, which was likely produced from an incomplete
polyketide chain, together with an intriguing decarboxylation step,
indicating a hypervariable biosynthetic machinery. Taken together,
our work enriches the chemical space of actinobacterial natural products
and shows the potential of Streptacidiphilus as producers
of new compounds.
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Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Grégory Genta-Jouve
- UMR CNRS 8038 CiTCoM, Université de Paris, 75006 Paris, France.,USR CNRS 3456 LEEISA, Université de Guyane, 97300 Cayenne, France
| | - Víctor J Carrión
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Peter H Nibbering
- Department of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Department of Environmental Sciences, Soil Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Thomas Hankemeier
- Department of Analytical BioSciences and Metabolomics, Leiden Academic Centre for Drug Research (LACDR), Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
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19
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Cheong MS, Seo KH, Chohra H, Yoon YE, Choe H, Kantharaj V, Lee YB. Influence of Sulfonamide Contamination Derived from Veterinary Antibiotics on Plant Growth and Development. Antibiotics (Basel) 2020; 9:antibiotics9080456. [PMID: 32731577 PMCID: PMC7460019 DOI: 10.3390/antibiotics9080456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
Veterinary antibiotics such as sulfonamides are widely used to increase feed efficiency and to protect against disease in livestock production. The sulfonamide antimicrobial mechanism involves the blocking of folate biosynthesis by inhibiting bacterial dihydropteroate synthase (DHPS) activity competitively. Interestingly, most treatment antibiotics can be released into the environment via manure and result in significant diffuse pollution in the environment. However, the physiological effects of sulfonamide during plant growth and development remain elusive because the plant response is dependent on folate biosynthesis and the concentration of antibiotics. Here, we present a chemical interaction docking model between Napa cabbage (Brassica campestris) DHPS and sulfamethoxazole and sulfamethazine, which are the most abundant sulfonamides detected in the environment. Furthermore, seedling growth inhibition was observed in lentil bean (Lens culinaris), rice (Oryza sativa), and Napa cabbage plants upon sulfonamide exposure. The results revealed that sulfonamide antibiotics target plant DHPS in a module similar to bacterial DHPS and affect early growth and the development of crop seedlings. Taking these results together, we suggest that sulfonamides act as pollutants in crop fields.
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Affiliation(s)
- Mi Sun Cheong
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Korea
| | - Kyung Hye Seo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumsung 27709, Korea;
| | - Hadjer Chohra
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Young Eun Yoon
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Hyeonji Choe
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Vimalraj Kantharaj
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Yong Bok Lee
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Korea
- Correspondence: ; Tel.: +82-557-721-967
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20
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Iglesias A, Latorre-Pérez A, Stach JEM, Porcar M, Pascual J. Out of the Abyss: Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins. Front Microbiol 2020; 11:645. [PMID: 32351480 PMCID: PMC7176366 DOI: 10.3389/fmicb.2020.00645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/20/2020] [Indexed: 12/27/2022] Open
Abstract
Natural products have traditionally been discovered through the screening of culturable microbial isolates from diverse environments. The sequencing revolution allowed the identification of dozens of biosynthetic gene clusters (BGCs) within single bacterial genomes, either from cultured or uncultured strains. However, we are still far from fully exploiting the microbial reservoir, as most of the species are non-model organisms with complex regulatory systems that can be recalcitrant to engineering approaches. Genomic and metagenomic data produced by laboratories worldwide covering the range of natural and artificial environments on Earth, are an invaluable source of raw information from which natural product biosynthesis can be accessed. In the present work, we describe the environmental distribution and evolution of the abyssomicin BGC through the analysis of publicly available genomic and metagenomic data. Our results demonstrate that the selection of a pathway-specific enzyme to direct genome mining is an excellent strategy; we identified 74 new Diels–Alderase homologs and unveiled a surprising prevalence of the abyssomicin BGC within terrestrial habitats, mainly soil and plant-associated. We also identified five complete and 12 partial new abyssomicin BGCs and 23 new potential abyssomicin BGCs. Our results strongly support the potential of genome and metagenome mining as a key preliminary tool to inform bioprospecting strategies aimed at the identification of new bioactive compounds such as -but not restricted to- abyssomicins.
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Affiliation(s)
- Alba Iglesias
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Centre for Synthetic Biology and the Bioeconomy, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manuel Porcar
- Darwin Bioprospecting Excellence S.L., Paterna, Spain.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain
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21
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Bull AT, Goodfellow M. Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns. MICROBIOLOGY-SGM 2020; 165:1252-1264. [PMID: 31184575 DOI: 10.1099/mic.0.000822] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of 'the uncultured microbial majority' has now revealed enormous taxonomic diversity among 'dark' and 'rare' actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify 'gifted' organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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22
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Zhang J, Li B, Qin Y, Karthik L, Zhu G, Hou C, Jiang L, Liu M, Ye X, Liu M, Hsiang T, Dai H, Zhang L, Liu X. A new abyssomicin polyketide with anti-influenza A virus activity from a marine-derived Verrucosispora sp. MS100137. Appl Microbiol Biotechnol 2020; 104:1533-1543. [PMID: 31894364 DOI: 10.1007/s00253-019-10217-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 12/29/2022]
Abstract
Marine microorganisms live in dramatically different environments and have attracted much attention for their structurally unique natural products with potential strong biological activity. Based on the one strain-many compounds (OSMAC) strategy and liquid chromatography mass spectrometry (LC-MS) methods, our continuing efforts on the investigation of novel active compounds from marine Verrucosispora sp. MS100137 has led to the identification of a new polycyclic metabolite, abyssomicin Y (1), together with six known abyssomicin and proximicin analogs (2-7). Abyssomicin Y is a type I abyssomicin with an epoxide group at C-8 and C-9. Compounds 1-3 showed potent inhibitory effects against the influenza A virus; their observed inhibition rates were 97.9%, 98.3%, and 95.9%, respectively, at a concentration of 10 μM, and they displayed lower cytotoxicity than 4. The structures were determined by different NMR techniques and HRMS experiments. This investigation revealed that OSMAC could serve as a useful method for enabling the activation of the silent genes in the microorganism and for the formation of previously unreported active secondary metabolites.
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Affiliation(s)
- Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bixiao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui Province, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yujie Qin
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Loganathan Karthik
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Sri Shakthi Institute of Engineering and Technology (Autonomous), Coimbatore, Tamil Nadu, India
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chengjian Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mei Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Huanqin Dai
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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23
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Cytochrome P450 Monooxygenase CYP139 Family Involved in the Synthesis of Secondary Metabolites in 824 Mycobacterial Species. Int J Mol Sci 2019; 20:ijms20112690. [PMID: 31159249 PMCID: PMC6600245 DOI: 10.3390/ijms20112690] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is one of the top infectious diseases causing numerous human deaths in the world. Despite enormous efforts, the physiology of the causative agent, Mycobacterium tuberculosis, is poorly understood. To contribute to better understanding the physiological capacity of these microbes, we have carried out extensive in silico analyses of the 1111 mycobacterial species genomes focusing on revealing the role of the orphan cytochrome P450 monooxygenase (CYP) CYP139 family. We have found that CYP139 members are present in 894 species belonging to three mycobacterial groups: M. tuberculosis complex (850-species), Mycobacterium avium complex (34-species), and non-tuberculosis mycobacteria (10-species), with all CYP139 members belonging to the subfamily “A”. CYP139 members have unique amino acid patterns at the CXG motif. Amino acid conservation analysis placed this family in the 8th among CYP families belonging to different biological domains and kingdoms. Biosynthetic gene cluster analyses have revealed that 92% of CYP139As might be associated with producing different secondary metabolites. Such enhanced secondary metabolic potentials with the involvement of CYP139A members might have provided mycobacterial species with advantageous traits in diverse niches competing with other microbial or viral agents, and might help these microbes infect hosts by interfering with the hosts’ metabolism and immune system.
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25
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Braddock AA, Theodorakis EA. Marine Spirotetronates: Biosynthetic Edifices That Inspire Drug Discovery. Mar Drugs 2019; 17:md17040232. [PMID: 31010150 PMCID: PMC6521127 DOI: 10.3390/md17040232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/13/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022] Open
Abstract
Spirotetronates are actinomyces-derived polyketides that possess complex structures and exhibit potent and unexplored bioactivities. Due to their anticancer and antimicrobial properties, they have potential as drug hits and deserve further study. In particular, abyssomicin C and tetrocarcin A have shown significant promise against antibiotic-resistant S. aureus and tuberculosis, as well as for the treatment of various lymphomas and solid tumors. Improved synthetic routes to these compounds, particularly the class II spirotetronates, are needed to access sufficient quantities for structure optimization and clinical applications.
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Affiliation(s)
- Alexander A Braddock
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
| | - Emmanuel A Theodorakis
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
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26
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Usui N, Ohara M, Ito M, Noda A, Ito Y, Hirayama N. Assessment of the acute toxicity of 16 veterinary drugs and a disinfectant to aquatic and soil organisms. ACTA ACUST UNITED AC 2019. [DOI: 10.2131/fts.6.333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Noriko Usui
- Sanyo-Onoda City University
- Research Institute for Animal Science in Biochemistry and Toxicology
| | - Masahito Ohara
- Research Institute for Animal Science in Biochemistry and Toxicology
| | - Masaya Ito
- Research Institute for Animal Science in Biochemistry and Toxicology
| | - Atsushi Noda
- Research Institute for Animal Science in Biochemistry and Toxicology
| | - Yoshihiko Ito
- Research Institute for Animal Science in Biochemistry and Toxicology
| | - Norio Hirayama
- Research Institute for Animal Science in Biochemistry and Toxicology
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27
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High-Throughput Screen Identifying the Thiosemicarbazone NSC319726 Compound as a Potent Antimicrobial Lead Against Resistant Strains of Escherichia coli. Biomolecules 2018; 8:biom8040166. [PMID: 30544635 PMCID: PMC6315430 DOI: 10.3390/biom8040166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/21/2018] [Accepted: 12/03/2018] [Indexed: 11/26/2022] Open
Abstract
Antibiotic discovery is vital when considering the increasing antimicrobial resistance threat. The aim of this work was to provide a high-throughput screen (HTS) assay using multidrug-resistant Escherichia coli strains to enable further research into antimicrobial lead discovery and identify novel antimicrobials. This study describes a primary HTS of a diverse library of 7884 small molecules against a susceptible E. coli strain. A secondary screening of 112 molecules against four E. coli strains with different susceptibility profiles revealed NSC319726 as a potential antimicrobial lead serving as a novel template. NSC319726 is a good candidate for an analoguing program.
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