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Wang H, Yang Y, Abe I. Modifications of Prenyl Side Chains in Natural Product Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202415279. [PMID: 39363683 DOI: 10.1002/anie.202415279] [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: 08/10/2024] [Revised: 10/01/2024] [Accepted: 10/01/2024] [Indexed: 10/05/2024]
Abstract
In recent years, there has been a growing interest in understanding the enzymatic machinery responsible for the modifications of prenyl side chains and elucidating their roles in natural product biosynthesis. This interest stems from the pivotal role such modifications play in shaping the structural and functional diversity of natural products, as well as from their potential applications to synthetic biology and drug discovery. In addition to contributing to the diversity and complexity of natural products, unique modifications of prenyl side chains are represented by several novel biosynthetic mechanisms. Representative unique examples of epoxidation, dehydrogenation, oxidation of methyl groups to carboxyl groups, unusual C-C bond cleavage and oxidative cyclization are summarized and discussed. By revealing the intriguing chemistry and enzymology behind these transformations, this comprehensive and comparative review will guide future efforts in the discovery, characterization and application of modifications of prenyl side chains in natural product biosynthesis.
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Affiliation(s)
- Huibin Wang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yi Yang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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2
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Nelson S, Parkinson EI. Synthetic-bioinformatic natural product-inspired peptides. Nat Prod Rep 2024. [PMID: 39479929 PMCID: PMC11525955 DOI: 10.1039/d4np00043a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Indexed: 11/02/2024]
Abstract
Covering: 2016 to 2024Natural products, particularly cyclic peptides, are a promising source of bioactive compounds. Nonribosomal peptide synthetases (NRPSs) play a key role in biosynthesizing these compounds, which include antibiotic and anticancer agents, immunosuppressants, and others. Traditional methods of discovering natural products have limitations including cryptic biosynthetic gene clusters (BGCs), low titers, and currently unculturable organisms. This has prompted the exploration of alternative approaches. Synthetic-bioinformatic natural products (syn-BNPs) are one such alternative that utilizes bioinformatics techniques to predict nonribosomal peptides (NRPs) followed by chemical synthesis of the predicted peptides. This approach has shown promise, resulting in the discovery of a variety of bioactive compounds including peptides with antibacterial, antifungal, anticancer, and proteasome-stimulating activities. Despite the success of this approach, challenges remain especially in the accurate prediction of fatty acid incorporation, tailoring enzyme modifications, and peptide release mechanisms. Further work in these areas will enable the discovery of many bioactive peptides that are currently inaccessible.
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Affiliation(s)
- Samantha Nelson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
| | - Elizabeth I Parkinson
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47906, USA.
- James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, USA
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3
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Tjallinks G, Mattevi A, Fraaije MW. Biosynthetic Strategies of Berberine Bridge Enzyme-like Flavoprotein Oxidases toward Structural Diversification in Natural Product Biosynthesis. Biochemistry 2024; 63:2089-2110. [PMID: 39133819 PMCID: PMC11375781 DOI: 10.1021/acs.biochem.4c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
Berberine bridge enzyme-like oxidases are often involved in natural product biosynthesis and are seen as essential enzymes for the generation of intricate pharmacophores. These oxidases have the ability to transfer a hydride atom to the FAD cofactor, which enables complex substrate modifications and rearrangements including (intramolecular) cyclizations, carbon-carbon bond formations, and nucleophilic additions. Despite the diverse range of activities, the mechanistic details of these reactions often remain incompletely understood. In this Review, we delve into the complexity that BBE-like oxidases from bacteria, fungal, and plant origins exhibit by providing an overview of the shared catalytic features and emphasizing the different reactivities. We propose four generalized modes of action by which BBE-like oxidases enable the synthesis of natural products, ranging from the classic alcohol oxidation reactions to less common amine and amide oxidation reactions. Exploring the mechanisms utilized by nature to produce its vast array of natural products is a subject of considerable interest and can lead to the discovery of unique biochemical activities.
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Affiliation(s)
- Gwen Tjallinks
- Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Groningen 9747 AG, The Netherlands
- Department
of Biology and Biotechnology, University
of Pavia, Pavia 27100, Italy
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University
of Pavia, Pavia 27100, Italy
| | - Marco W. Fraaije
- Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Groningen 9747 AG, The Netherlands
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4
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Chandole PK, Pawar TJ, Olivares-Romero JL, Tivari SR, Garcia Lara B, Patel H, Ahmad I, Delgado-Alvarado E, Kokate SV, Jadeja Y. Exploration of novel cationic amino acid-enriched short peptides: design, SPPS, biological evaluation and in silico study. RSC Adv 2024; 14:17710-17723. [PMID: 38832247 PMCID: PMC11145139 DOI: 10.1039/d3ra08313f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/28/2024] [Indexed: 06/05/2024] Open
Abstract
Antimicrobial resistance (AMR) represents a critical challenge worldwide, necessitating the pursuit of novel approaches to counteract bacterial and fungal pathogens. In this context, we explored the potential of cationic amino acid-enriched short peptides, synthesized via solid-phase methods, as innovative antimicrobial candidates. Our comprehensive evaluation assessed the antibacterial and antifungal efficacy of these peptides against a panel of significant pathogens, including Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Candida albicans, and Aspergillus niger. Utilizing molecular docking techniques, we delved into the molecular interactions underpinning the peptides' action against these microorganisms. The results revealed a spectrum of inhibitory activities, with certain peptide sequences displaying pronounced effectiveness across various pathogens. These findings underscore the peptides' potential as promising antimicrobial agents, with molecular docking offering valuable insights into their mechanisms of action. This study enriches antimicrobial peptide (AMP) research by identifying promising candidates for further refinement and development toward therapeutic application, highlighting their significance in addressing the urgent issue of AMR.
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Affiliation(s)
| | - Tushar Janardan Pawar
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351 Xalapa 91073 Veracruz Mexico
| | - José Luis Olivares-Romero
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351 Xalapa 91073 Veracruz Mexico
| | - Sunil R Tivari
- Department of Chemistry, Marwadi University Rajkot-360003 Gujarat India
| | - Bianney Garcia Lara
- Departamento de Química, Universidad de Guanajuato Noria Alta S/N Guanajuato-36050 Guanajuato Mexico
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research Shirpur District Dhule-425405 Maharashtra India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research Shirpur District Dhule-425405 Maharashtra India
| | - Enrique Delgado-Alvarado
- Micro and Nanotechnology Research Center, Universidad Veracruzana Blvd. Av. Ruiz Cortines No. 455 Fracc. Costa Verde Boca del Río 94294 Mexico
| | - Siddhant V Kokate
- Department of Chemistry, S. S. C. College Junnar Pune-410502 Maharashtra India
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5
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Dashti Y, Errington J. Chemistry and biology of specialized metabolites produced by Actinomadura. Nat Prod Rep 2024; 41:370-401. [PMID: 38099919 PMCID: PMC10951976 DOI: 10.1039/d3np00047h] [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: 10/09/2023] [Indexed: 03/21/2024]
Abstract
Covering: up to the end of 2022In recent years rare Actinobacteria have become increasingly recognised as a rich source of novel bioactive metabolites. Actinomadura are Gram-positive bacteria that occupy a wide range of ecological niches. This review highlights about 230 secondary metabolites produced by Actinomadura spp., reported until the end of 2022, including their bioactivities and selected biosynthetic pathways. Notably, the bioactive compounds produced by Actinomadura spp. demonstrate a wide range of activities, including antimicrobial, antitumor and anticoccidial effects, highlighting their potential in various fields.
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Affiliation(s)
- Yousef Dashti
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
| | - Jeff Errington
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
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Banerjee C, Barman R, Darshani P, Pillai M, Ahuja S, Mondal R, Pragadheesh VS, Chakraborty J, Kumar D. α-Viniferin, a dietary phytochemical, inhibits Monoamine oxidase and alleviates Parkinson's disease associated behavioral deficits in a mice model. Neurochem Int 2024; 174:105698. [PMID: 38364939 DOI: 10.1016/j.neuint.2024.105698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/31/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
Parkinson's disease (PD) is one of the most prevalent age-related neurodegenerative disorders. Behavioral complexities worsen over time due to progressive dopaminergic (DArgic) neuronal loss at substantia nigra region of brain. Available treatments typically aim to increase dopamine (DA) levels at striatum. DA is degraded by Monoamine oxidase (MAO), thus dietary phytochemicals with MAO inhibitory properties can contribute to elevate DA levels and reduce the ailment. Characterization of naturally occurring dietary MAO inhibitors is inadequate. Based on available knowledge, we selected different classes of molecules and conducted a screening process to assess their potential as MAO inhibitors. The compounds mostly derived from food sources, broadly belonging to triterpenoids (ursane, oleanane and hopane), alkaloid, polyphenolics, monoterpenoids, alkylbenzene, phenylpropanoid and aromatic alcohol classes. Among all the molecules, highest level of MAO inhibition is offered by α-viniferin, a resveratrol trimer. Cell viability, mitochondrial morphology and reactive oxygen species (ROS) generation remained unaltered by 50 μM α-viniferin treatment in-vitro. Toxicity studies in Drosophila showed unchanged gross neuronal morphology, ROS level, motor activity or long-term survival. α-Viniferin inhibited MAO in mice brain and elevated striatal DA levels. PD-related akinesia and cataleptic behavior were attenuated by α-viniferin due to increase in striatal DA. Our study implies that α-viniferin can be used as an adjunct phytotherapeutic agent for mitigating PD-related behavioral deterioration.
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Affiliation(s)
- Chayan Banerjee
- Cell Biology and Physiology Division, CSIR- Indian Institute of Chemical Biology, Kolkata- 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Raju Barman
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata- 700032, India
| | - Priya Darshani
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata- 700032, India
| | - Meghana Pillai
- Cell Biology and Physiology Division, CSIR- Indian Institute of Chemical Biology, Kolkata- 700032, India
| | - Sanchi Ahuja
- Cell Biology and Physiology Division, CSIR- Indian Institute of Chemical Biology, Kolkata- 700032, India
| | - Rupsha Mondal
- Cell Biology and Physiology Division, CSIR- Indian Institute of Chemical Biology, Kolkata- 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - V S Pragadheesh
- CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru- 560065, India
| | - Joy Chakraborty
- Cell Biology and Physiology Division, CSIR- Indian Institute of Chemical Biology, Kolkata- 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Deepak Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India; Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata- 700032, India.
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Willetts A. The Role of Dioxygen in Microbial Bio-Oxygenation: Challenging Biochemistry, Illustrated by a Short History of a Long Misunderstood Enzyme. Microorganisms 2024; 12:389. [PMID: 38399793 PMCID: PMC10891995 DOI: 10.3390/microorganisms12020389] [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: 01/02/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
A Special Issue of Microorganisms devoted to 'Microbial Biocatalysis and Biodegradation' would be incomplete without some form of acknowledgement of the many important roles that dioxygen-dependent enzymes (principally mono- and dioxygenases) play in relevant aspects of bio-oxygenation. This is reflected by the multiple strategic roles that dioxygen -dependent microbial enzymes play both in generating valuable synthons for chemoenzymatic synthesis and in facilitating reactions that help to drive the global geochemical carbon cycle. A useful insight into this can be gained by reviewing the evolution of the current status of 2,5-diketocamphane 1,2-monooxygenase (EC 1.14.14.108) from (+)-camphor-grown Pseudomonas putida ATCC 17453, the key enzyme that promotes the initial ring cleavage of this natural bicyclic terpene. Over the last sixty years, the perceived nature of this monooxygenase has transmogrified significantly. Commencing in the 1960s, extensive initial studies consistently reported that the enzyme was a monomeric true flavoprotein dependent on both FMNH2 and nonheme iron as bound cofactors. However, over the last decade, all those criteria have changed absolutely, and the enzyme is currently acknowledged to be a metal ion-independent homodimeric flavin-dependent two-component mono-oxygenase deploying FMNH2 as a cosubstrate. That transition is a paradigm of the ever evolving nature of scientific knowledge.
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Affiliation(s)
- Andrew Willetts
- 4 Sv Ivan, 21400 Sutivan, Croatia;
- Curnow Consultancies, Helston TR13 9PQ, UK
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8
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Meng Z, Tan Y, Duan YL, Li M. Monaspin B, a Novel Cyclohexyl-furan from Cocultivation of Monascus purpureus and Aspergillus oryzae, Exhibits Potent Antileukemic Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1114-1123. [PMID: 38166364 DOI: 10.1021/acs.jafc.3c08187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Natural products are a rich resource for the discovery of innovative drugs. Microbial cocultivation enables discovery of novel natural products through tandem enzymatic catalysis between different fungi. In this study, Monascus purpureus, as a food fermentation strain capable of producing abundant natural products, was chosen as an example of a cocultivation pair strain. Cocultivation screening revealed that M. purpureus and Aspergillus oryzae led to the production of two novel cyclohexyl-furans, Monaspins A and B. Optimization of the cocultivation mode and media enhanced the production of Monaspins A and B to 1.2 and 0.8 mg/L, respectively. Monaspins A and B were structurally elucidated by HR-ESI-MS and NMR. Furthermore, Monaspin B displayed potent antiproliferative activity against the leukemic HL-60 cell line by inducing apoptosis, with a half-maximal inhibitory concentration (IC50) of 160 nM. Moreover, in a mouse leukemia model, Monaspin B exhibited a promising in vivo antileukemic effect by reducing white blood cell, lymphocyte, and neutrophil counts. Collectively, these results indicate that Monaspin B is a promising candidate agent for leukemia therapy.
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Affiliation(s)
- Zitong Meng
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, Tongji Medical College, Huazhong University of Science and Technology, Hangkong Road 13, Wuhan 430030, China
| | - Yingao Tan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Ya-Li Duan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
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Alexander AK, Elshahawi SI. Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization. Chembiochem 2023; 24:e202300372. [PMID: 37338668 PMCID: PMC10496146 DOI: 10.1002/cbic.202300372] [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: 05/18/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.
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Affiliation(s)
- Ashley K Alexander
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
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