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Rodríguez-Caro JF, Afonso MM, Palenzuela JA. A Simple Entry to the 5,8-Disubstituted Indolizidine Skeleton via Hetero Diels-Alder Reaction. Molecules 2023; 28:7316. [PMID: 37959735 PMCID: PMC10647431 DOI: 10.3390/molecules28217316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The 5,8-disubstituted indolizidines are the largest family of indolizidines isolated from the skin of amphibians. These compounds exhibit interesting biological activities such as noncompetitive blockers of nicotinic receptors. In this paper, we present a short, simple, and general synthesis of these alkaloids based on the hetero Diels-Alder reaction between suitable monoactivated dienes and Δ1-pyrroline as the dienophile. The selectivity of the process is explained based on computational studies. Concise synthesis of the indolizidine alkaloid 181B from a hetero Diels-Alder reaction was accomplished in four steps.
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Affiliation(s)
| | - María M. Afonso
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González (SINTESTER), Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez 2, 38206 La Laguna, Spain;
| | - José Antonio Palenzuela
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González (SINTESTER), Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez 2, 38206 La Laguna, Spain;
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Manochkumar J, Cherukuri AK, Kumar RS, Almansour AI, Ramamoorthy S, Efferth T. A critical review of machine-learning for "multi-omics" marine metabolite datasets. Comput Biol Med 2023; 165:107425. [PMID: 37696182 DOI: 10.1016/j.compbiomed.2023.107425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
During the last decade, genomic, transcriptomic, proteomic, metabolomic, and other omics datasets have been generated for a wide range of marine organisms, and even more are still on the way. Marine organisms possess unique and diverse biosynthetic pathways contributing to the synthesis of novel secondary metabolites with significant bioactivities. As marine organisms have a greater tendency to adapt to stressed environmental conditions, the chance to identify novel bioactive metabolites with potential biotechnological application is very high. This review presents a comprehensive overview of the available "-omics" and "multi-omics" approaches employed for characterizing marine metabolites along with novel data integration tools. The need for the development of machine-learning algorithms for "multi-omics" approaches is briefly discussed. In addition, the challenges involved in the analysis of "multi-omics" data and recommendations for conducting "multi-omics" study were discussed.
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Affiliation(s)
- Janani Manochkumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Aswani Kumar Cherukuri
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 632014, India
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Siva Ramamoorthy
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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Liu WL, Yang ZW, Guo DY, Deng QQ, Li JL, Wang PD, Chen SH, Liu L, Nie GX, Li WJ. Cereibacter flavus sp. nov., a novel member of the family Rhodobacteraceae isolated from seawater of the South China Sea and reclassification of Rhodobacter alkalitolerans as Cereibacter alkalitolerans comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37773605 DOI: 10.1099/ijsem.0.006051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023] Open
Abstract
A Gram-stain-negative, aerobic, motile, ovoid-shaped and yellow-coloured strain, designated SYSU M79828T, was isolated from seawater collected from the South China Sea. Growth of this strain was observed at 4-37 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-6% NaCl (optimum, 3.0 %, w/v). The respiratory quinone was found to be Q-10. Major fatty acid constituents were C18 : 1 ω7c/C18 : 1 ω6c, C18 : 1 ω7c11-methyl and C18 : 0 (>5 % of total). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, two unidentified phospholipid, one unidentified lipid and an unidentified glycolipid. The genomic DNA G+C content was 64.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M79828T belonged to the genus Cereibacter and had the highest sequences similarity to 'Rhodobacter xinxiangensis' TJ48T (98.41 %). Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterizations, we consider that strain SYSU M79828T represents a novel species of the genus Cereibacter, for which the name Cereibacter flavus sp. nov. is proposed. The type strain is SYSU M79828T (=GDMCC 1.3803T=KCTC 92893T). In addition, according to the results of phylogenetic analysis and similar taxonomic characteristics, we propose that Rhodobacter alkalitolerans should be reclassified as Cereibacter alkalitolerans comb. nov.
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Affiliation(s)
- Wen-Li Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Dan-Yuan Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Sen-Hua Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Laila A, Setiawan F, Widyastuti W, Fadhilah MR, Setiawan A, Juliasih NLGR, Setiawan WA, Apriliana E, Ahmadi P, Arai M, Hendri J. Exploration and Biorefinery Antimicrobial Agent through Solid State Fermentation from Indonesia’s Marine Actinomycetes. Fermentation 2023. [DOI: 10.3390/fermentation9040334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
This study aimed to obtain novel bioactive compounds derived from actinomycetes associated with marine biota from the coast of Indonesia. Actinomycetes have been identified as a potential source of bioactive compounds through enzymatic fermentation. In order to obtain bioactive compounds from the results of the biorefinery process, cultivation was performed by solid state fermentation (SSF) on shrimp shell waste medium. The inhibitory activity against pathogenic microorganisms was measured based on the optical density of samples from Gorontalo and Buleleng, Bali, Indonesia. Six isolates had a clear zone as an indicator of the chitinase activity of chitinase enzymes. The SSF extract, obtained after 14 days of incubation, was assayed for its antimicrobial activity by the 96-well plate microtiter method. Among the six isolates, isolate 19B19A1 had antibacterial and antifungal activity against Staphylococcus aureus and Malassezia globosa, respectively. DNA analysis indicated that the 19B19A1 isolate was Streptomyces tritolerans 19B19A1 and that its extract contained an alkaloid component that played a role in antimicrobial activity. These results indicate that shrimp shells can be used as a nutrient-rich alternative culture medium for actinomycetes. This study is expected to become a source of information related to biorefinery, especially in the exploration of bioactive compounds produced by actinomycetes.
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El-Sawy ER, El-Shahid ZA, Soliman AAF, Nassrallah A, Abdelwahab AB, Kirsch G, Abdelmegeed H. Synthetic Analogs of Marine Alkaloid Aplysinopsin Suppress Anti-Apoptotic Protein BCL2 in Prostate Cancer. Molecules 2022; 28:molecules28010109. [PMID: 36615305 PMCID: PMC9821956 DOI: 10.3390/molecules28010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022]
Abstract
Aplysinopsins are a class of indole alkaloids that possess various pharmacological activities. Although their action has been studied in regard to many diseases, their effect on prostate cancer has not yet been examined. Therefore, we synthesized a new series of aplysinopsin analogs and investigated their cytotoxic activity against prostate cancer. Five analogs showed high antitumor activity via suppressing the expression of the anti-apoptotic gene Bcl2, simulationously increasing the expression of the pro-apoptotic genes p53, Bax and Caspase 3. The inhibition of BCL2 led to the activation of BAX, which in turn activated Caspase 3, leading to apoptosis. This dual mechanism of action via apoptosis and cell cycle arrest induction is responsible for aplysinopsin analogs antitumor activity. Hence, our newly synthesized analogs are highly promising candidates for further preclinical studies against prostate cancer.
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Affiliation(s)
- Eslam R. El-Sawy
- Chemistry of Natural Compounds Department, National Research Centre, Giza 12622, Egypt
- Correspondence: (E.R.E.-S.); (G.K.); (H.A.); Tel.: (+33)-03-72-74-92-00 (G.K.); Fax: (+33)-03-72-74-91-87
| | - Zeinab A. El-Shahid
- Chemistry of Natural and Microbial Products Department, National Research Centre, Giza 12622, Egypt
| | - Ahmed A. F. Soliman
- Drug Bioassay-Cell Culture Laboratory, Pharmacognosy Department, National Research Center, Giza 12622, Egypt
| | - Amr Nassrallah
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | | | - Gilbert Kirsch
- Laboratoire Lorrain de Chimie Moléculaire (L.2.C.M.), Université de Lorraine, 57050 Metz, France
- Correspondence: (E.R.E.-S.); (G.K.); (H.A.); Tel.: (+33)-03-72-74-92-00 (G.K.); Fax: (+33)-03-72-74-91-87
| | - Heba Abdelmegeed
- Chemistry of Natural Compounds Department, National Research Centre, Giza 12622, Egypt
- Correspondence: (E.R.E.-S.); (G.K.); (H.A.); Tel.: (+33)-03-72-74-92-00 (G.K.); Fax: (+33)-03-72-74-91-87
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Liu JR, Liu JM, Gao Y, Shi Z, Nie KR, Guo D, Deng F, Zhang HF, Ali AS, Zhang MZ, Zhang WH, Gu YC. Discovery of Novel Pimprinine and Streptochlorin Derivatives as Potential Antifungal Agents. Mar Drugs 2022; 20. [PMID: 36547887 DOI: 10.3390/md20120740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Pimprinine and streptochlorin are indole alkaloids derived from marine or soil microorganisms. In our previous study, they were promising lead compounds due to their potent bioactivity in preventing many phytopathogens, but further structural modifications are required to improve their antifungal activity. In this study, pimprinine and streptochlorin were used as parent structures with the combination strategy of their structural features. Three series of target compounds were designed and synthesized. Subsequent evaluation for antifungal activity against six common phytopathogenic fungi showed that some of thee compounds possessed excellent effects, and this is highlighted by compounds 4a and 5a, displaying 99.9% growth inhibition against Gibberella zeae and Alternaria Leaf Spot under 50 μg/mL, respectively. EC50 values indicated that compounds 4a, 5a, 8c, and 8d were even more active than Azoxystrobin and Boscalid. SAR analysis revealed the relationship between 5-(3'-indolyl)oxazole scaffold and antifungal activity, which provides useful insight into the development of new target molecules. Molecular docking models indicate that compound 4a binds with leucyl-tRNA synthetase in a similar mode as AN2690, offering a perspective on the mode of action for the study of its antifungal activity. These results suggest that compounds 4a and 5a could be regarded as novel and promising antifungal agents against phytopathogens due to their valuable potency.
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Xiao S, Chen N, Chai Z, Zhou M, Xiao C, Zhao S, Yang X. Secondary Metabolites from Marine-Derived Bacillus: A Comprehensive Review of Origins, Structures, and Bioactivities. Mar Drugs 2022; 20:567. [PMID: 36135756 PMCID: PMC9501603 DOI: 10.3390/md20090567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The marine is a highly complex ecosystem including various microorganisms. Bacillus species is a predominant microbialflora widely distributed in marine ecosystems. This review aims to provide a systematic summary of the newly reported metabolites produced by marine-derived Bacillus species over recent years covering the literature from 2014 to 2021. It describes the structural diversity and biological activities of the reported compounds. Herein, a total of 87 newly reported metabolites are included in this article, among which 49 compounds originated from marine sediments, indicating that marine sediments are majority sources of productive strains of Bacillus species Therefore, marine-derived Bacillus species are a potentially promising source for the discovery of new metabolites.
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