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Tang J, Lu F, Zhang X, Gao Z, Gong S, Zhang E. Backbone-Enabled and Ester Groups Switched δ-C(sp 2)-H Amination/Fluorination: Cyclic Dipeptides Synthesis. Org Lett 2024; 26:5130-5135. [PMID: 38843448 DOI: 10.1021/acs.orglett.4c01540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
An efficient and concise strategy for the synthesis of cyclic dipeptides via Pd-catalyzed site-selective δ-C(sp2)-H amination/fluorination and N-to-C cyclization is disclosed. The backbone amides within the dipeptides serves as endogenous directing groups, while the desired products were switched by the C-terminal ester group. This chemistry presents a novel and robust alternative to construct cyclodipeptide fragments.
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Affiliation(s)
- Jian Tang
- Key Laboratory of Catalytic Conversion and Clean Energy in Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
- Shengzhou Innovation Research Institute, Zhejiang Sci-Tech University, Shengzhou 312400, P. R. China
| | - Fengjie Lu
- Key Laboratory of Catalytic Conversion and Clean Energy in Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Xinyi Zhang
- Key Laboratory of Catalytic Conversion and Clean Energy in Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Zhenqi Gao
- Key Laboratory of Catalytic Conversion and Clean Energy in Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Shuo Gong
- Key Laboratory of Catalytic Conversion and Clean Energy in Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Ensheng Zhang
- Key Laboratory of Catalytic Conversion and Clean Energy in Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
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Kanikarapu S, Prasad R, Sethi M, Sahoo AK. Gold(I)-catalysed cyclisation of ( E)-ketene- N, O-acetals: a synthetic route toward spiro-oxazole-γ-lactones. Org Biomol Chem 2024; 22:4672-4679. [PMID: 38805239 DOI: 10.1039/d4ob00551a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In this study, we developed a cascade 5,5-cyclisation of internal ketene-N,O-acetals utilizing homogeneous Au(I) catalysis. This process involves an initial 5-exo-dig carbocyclisation, followed by a 5-exo-dig heterocyclisation that stereoselectively incorporates the O-atom of a water molecule into an N-tethered propargyl alkyne. This sequential reaction results in the formation of one C-C, two C-O, and two C-I bonds, ultimately leading to the synthesis of spiro-α-iodo-γ-lactone structures featuring oxazole rings in good yields.
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Affiliation(s)
- Suresh Kanikarapu
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
| | - Rangu Prasad
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
| | - Manoj Sethi
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
| | - Akhila K Sahoo
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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3
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Hu L, Lin J, Qin F, Xu L, Luo L. Exploring Sources, Biological Functions, and Potential Applications of the Ubiquitous Marine Cyclic Dipeptide: A Concise Review of Cyclic Glycine-Proline. Mar Drugs 2024; 22:271. [PMID: 38921582 PMCID: PMC11205142 DOI: 10.3390/md22060271] [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: 05/14/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Cyclic glycine-proline (cGP), a prevalent marine cyclic dipeptide, possesses a distinct pyrrolidine-2,5-dione scaffold, which contributes to the chemical diversity and broad bioactivities of cGP. The diverse sources from marine-related, endogenous biological, and synthetic pathways and the in vitro and in vivo activities of cGP are reviewed. The potential applications for cGP are also explored. In particular, the pivotal roles of cGP in regulating insulin-like growth factor-1 homeostasis, enhancing neuroprotective effects, and improving neurotrophic function in central nervous system diseases are described. The potential roles of this endogenous cyclic peptide in drug development and healthcare initiatives are also highlighted. This review underscores the significance of cGP as a fundamental building block in drug discovery with exceptional drug-like properties and safety. By elucidating the considerable value of cGP, this review aims to reignite interest in cGP-related research within marine medicinal chemistry and synthetic biology.
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Affiliation(s)
- Lei Hu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Jing Lin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Fei Qin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Li Xu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Lianzhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
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Son J, Hong Y, Seong H, Oh YS, Kwak MK. The high-throughput solid-phase extraction of cis-cyclo(L-Leu-L-Pro) and cis-cyclo(L-Phe-L-Pro) from Lactobacillus plantarum demonstrates efficacy against multidrug-resistant bacteria and influenza A (H3N2) virus. Front Mol Biosci 2024; 11:1346598. [PMID: 38828395 PMCID: PMC11140067 DOI: 10.3389/fmolb.2024.1346598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/19/2024] [Indexed: 06/05/2024] Open
Abstract
Introduction: 2,5-diketopiperazines are the simplest forms of cyclic dipeptides (CDPs) and have diverse frameworks with chiral side chains that are useful for drug development. Previous research has investigated the antimicrobial properties of proline-linked CDPs and their combinations in the culture filtrate (CF) of Lactobacillus plantarum LBP-K10 using anion exchange chromatography (AEC). However, the quantity of CDPs showcasing notable anti-influenza virus activity derived from AECs was generally lower than those originating from Lactobacillus CF. Methods: To address this issue, the study aims to propose a more efficient method for isolating CDPs and to introduce the antiviral combinations of CDPs obtained using a new method. The study employed a novel technique entailing high-throughput C18-based solid-phase extraction with a methanol gradient (MeSPE). The MeSPE method involved increasing the methanol concentration from 5% to 50% in 5% increments. Results: The methanol SPE fractions (MeSPEfs) eluted with methanol concentrations between 35% and 45% evinced substantial efficacy in inhibiting the influenza A/H3N2 virus via plaque-forming assay. MeSPEf-45, the 45% MeSPEf, exhibited exceptional efficacy in preventing viral infections in Madin-Darby kidney cells, surpassing both individual CDPs and the entire set of MeSPEfs. To identify the specific antiviral components of MeSPEf-45, all MeSPEfs were further fractionated through preparative high-performance liquid chromatography (prep-HPLC). MeSPEf-45 fractions S8 and S11 presented the highest activity against multidrug-resistant bacteria and influenza A/H3N2 virus among all MeSPEfs, with 11 common fractions. Antiviral fractions S8 and S11 were identified as proline-based CDPs, specifically cis-cyclo(L-Leu-L-Pro) and cis-cyclo(L-Phe-L-Pro), using gas chromatography-mass spectrometry. The combination of MeSPEf-45 fractions S8 and S11 displayed superior antibacterial and anti-influenza virus effects compared to the individual fractions S8 and S11. Discussion: High-throughput MeSPE-derived MeSPEfs and subsequent HPLC-fractionated fractions presents an innovative approach to selectively purify large amounts of potent antimicrobial CDPs from bacterial CF. The findings also show the effectiveness of physiologically bioactive combinations that utilize fractions not containing CDP. This study provides the initial evidence demonstrating the antimicrobial properties of CDPs acquired through high-throughput SPE techniques.
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Affiliation(s)
- Jaeyoung Son
- Laboratory of Microbial Physiology and Biotechnology, Department of Food and Nutrition, Institute of Food and Nutrition Science, College of Bio-Convergence, Eulji University, Seongnam, Republic of Korea
| | - Yeonju Hong
- Laboratory of Microbial Physiology and Biotechnology, Department of Food and Nutrition, Institute of Food and Nutrition Science, College of Bio-Convergence, Eulji University, Seongnam, Republic of Korea
| | - Hyeri Seong
- Laboratory of Microbial Physiology and Biotechnology, Department of Food and Nutrition, Institute of Food and Nutrition Science, College of Bio-Convergence, Eulji University, Seongnam, Republic of Korea
| | - Yoon Sin Oh
- Department of Food and Nutrition, Institute of Food and Nutrition Science, College of Bio-Convergence, Eulji University, Seongnam, Republic of Korea
| | - Min-Kyu Kwak
- Laboratory of Microbial Physiology and Biotechnology, Department of Food and Nutrition, Institute of Food and Nutrition Science, College of Bio-Convergence, Eulji University, Seongnam, Republic of Korea
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Pham MT, Yang FL, Liu IC, Liang PH, Lin HC. Non-Heme Iron Enzymes Catalyze Heterobicyclic and Spirocyclic Isoquinolone Core Formation in Piperazine Alkaloid Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202401324. [PMID: 38499463 DOI: 10.1002/anie.202401324] [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: 01/19/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
We report the discovery and biosynthesis of new piperazine alkaloids-arizonamides, and their derived compounds-arizolidines, featuring heterobicyclic and spirocyclic isoquinolone skeletons, respectively. Their biosynthetic pathway involves two crucial non-heme iron enzymes, ParF and ParG, for core skeleton construction. ParF has a dual function facilitating 2,3-alkene formation of helvamide, as a substrate for ParG, and oxidative cleavage of piperazine. Notably, ParG exhibits catalytic versatility in multiple oxidative reactions, including cyclization and ring reconstruction. A key amino acid residue Phe67 was characterized to control the formation of the constrained arizonamide B backbone by ParG.
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Affiliation(s)
- Mai-Truc Pham
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan R.O.C
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
| | - I-Chen Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
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6
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Ma C, Wang W, Zhang K, Zhang F, Chang Y, Sun C, Che Q, Zhu T, Zhang G, Li D. Exploring the Diverse Landscape of Fungal Cytochrome P450-Catalyzed Regio- and Stereoselective Dimerization of Diketopiperazines. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2310018. [PMID: 38687842 DOI: 10.1002/advs.202310018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/16/2024] [Indexed: 05/02/2024]
Abstract
Dimeric indole-containing diketopiperazines (di-DKPs) are a diverse group of natural products produced through cytochrome P450-catalyzed C-C or C-N coupling reactions. The regio- and stereoselectivity of these reactions plays a significant role in the structural diversity of di-DKPs. Despite their pivotal role, the mechanisms governing the selectivity in fungi are not fully understood. Employing bioinformatics analysis and heterologous expression experiments, five undescribed P450 enzymes (AmiP450, AcrP450, AtP450, AcP450, and AtuP450) responsible for the regio- and stereoselective dimerization of diketopiperazines (DKPs) in fungi are identified. The function of these P450s is consistent with phylogenetic analysis, highlighting their dominant role in controlling the dimerization modes. Combinatorial biosynthesis-based pathway reconstitution of non-native gene clusters expands the chemical space of fungal di-DKPs and reveals that the regioselectivity is influenced by the substrate. Furthermore, multiple sequence alignment and molecular docking of these enzymes demonstrate a C-terminal variable region near the substrate tunnel entrance in AtuP450 that is crucial for its regioselectivity. These findings not only reveal the secret of fungal di-DKPs diversity but also deepen understanding of the mechanisms and catalytic specificity involved in P450-catalyzed dimerization reactions.
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Affiliation(s)
- Chuanteng Ma
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Wenxue Wang
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Kaijin Zhang
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Falei Zhang
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Yimin Chang
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Chunxiao Sun
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Qian Che
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Dehai Li
- Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Qingdao/Sanya, 266000, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
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7
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Andreas MP, Giessen TW. Cyclodipeptide oxidase is an enzyme filament. Nat Commun 2024; 15:3574. [PMID: 38678027 PMCID: PMC11055893 DOI: 10.1038/s41467-024-48030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
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Affiliation(s)
- Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Wu M, Janzen DJ, Guan Z, Ye Y, Zhang Y, Li SM. The Promiscuous Flavin-Dependent Monooxygenase PboD from Aspergillus ustus Increases the Structural Diversity of Hydroxylated Pyrroloindoline Diketopiperazines. JOURNAL OF NATURAL PRODUCTS 2024; 87:1171-1178. [PMID: 38557026 DOI: 10.1021/acs.jnatprod.4c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The potential of natural products as pharmaceutical and agricultural agents is based on their large structural diversity, resulting in part from modifications of the backbone structure by tailoring enzymes during biosynthesis. Flavin-dependent monooxygenases (FMOs), as one such group of enzymes, play an important role in the biosynthesis of diverse natural products, including cyclodipeptide (CDP) derivatives. The FMO PboD was shown to catalyze C-3 hydroxylation at the indole ring of cyclo-l-Trp-l-Leu in the biosynthesis of protubonines, accompanied by pyrrolidine ring formation. PboD substrate promiscuity was investigated in this study by testing its catalytic activity toward additional tryptophan-containing CDPs in vitro and biotransformation in Aspergillus nidulans transformants bearing a truncated protubonine gene cluster with pboD and two acetyltransferase genes. High acceptance of five CDPs was detected for PboD, especially of those with a second aromatic moiety. Isolation and structure elucidation of five pyrrolidine diketopiperazine products, with two new structures, proved the expected stereospecific hydroxylation and pyrrolidine ring formation. Determination of kinetic parameters revealed higher catalytic efficiency of PboD toward three CDPs consisting of aromatic amino acids than of its natural substrate cyclo-l-Trp-l-Leu. In the biotransformation experiments with the A. nidulans transformant, modest formation of hydroxylated and acetylated products was also detected.
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Affiliation(s)
- Meiting Wu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Strasse 4, Marburg 35037, Germany
| | - Daniel J Janzen
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Strasse 4, Marburg 35037, Germany
| | - Zhenhua Guan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Ye
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Strasse 4, Marburg 35037, Germany
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9
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Zhou TP, Feng J, Wang Y, Li S, Wang B. Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS AU 2024; 4:1591-1604. [PMID: 38665654 PMCID: PMC11040706 DOI: 10.1021/jacsau.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (-)-naseseazine C (2) through intramolecular C-N bond formation and intermolecular C-C coupling. A thorough understanding of its catalytic mechanism is crucial for the engineering or design of P450-catalyzed C-N dimerization reactions. By employing MD simulations, QM/MM calculations, and enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that the most favorable pathway entails the transfer of a hydrogen atom from N7-H to Cpd I. Subsequently, there is a conformational change in the substrate radical, shifting it from the Re-face to the Si-face of N7 in Substrate 1. The Si-face conformation of Substrate 1 is stabilized by the protein environment and the π-π stacking interaction between the indole ring and heme porphyrin. The subsequent intermolecular C3-C6' bond formation between Substrate 1 radical and Substrate 2 occurs via a radical attack mechanism. The conformational switch of the Substrate 1 radical not only lowers the barrier of the intermolecular C3-C6' bond formation but also yields the correct stereoselectivity observed in experiments. In addition, we evaluated the reactivity of the ferric-superoxide species, showing it is not reactive enough to initiate the hydrogen atom abstraction from the indole NH group of the substrate. Our simulation provides a comprehensive mechanistic insight into how the P450 enzyme precisely controls both the intramolecular C-N cyclization and intermolecular C-C coupling. The current findings align with the available experimental data, emphasizing the pivotal role of substrate dynamics in governing P450 catalysis.
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Affiliation(s)
- Tai-Ping Zhou
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianqiang Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yongchao Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shengying Li
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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10
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Kundu S, Maji MS. Solution-Phase Late-Stage Chemoselective Photocatalytic Removal of Sulfonyl and Phenacyl Groups in Peptides. Chemistry 2024; 30:e202400033. [PMID: 38345998 DOI: 10.1002/chem.202400033] [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: 01/04/2024] [Indexed: 03/07/2024]
Abstract
Herein, BPC catalyzed visible-light-triggered target-specific late-stage solution phase desulfonylation from tryptophan in oligopeptides is portrayed by overcoming the isolation issue up to octamers. This robust and mild method is highly predictable and chemoselective, tolerating myriad of functional groups in aza-heteroaromatics and peptides. Interestingly, reductive desulfonylation is also amenable to biologically significant reactive histidine and tyrosine side chains, signifying the versatility of the strategy. Additional efficacy of BPC is demonstrated by solution phase phenacyl deprotection from C-terminal in peptides. Furthermore, excellent catalyst loading of 0.5 mol% and recyclability demonstrate the practical utility and applicability of this strategy.
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Affiliation(s)
- Samrat Kundu
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Modhu Sudan Maji
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
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11
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González JF, Dea-Ayuela MA, Huck L, Orduña JM, Bolás-Fernández F, de la Cuesta E, Haseen N, Mohammed AA, Menéndez JC. Dual Antitubercular and Antileishmanial Profiles of Quinoxaline Di- N-Oxides Containing an Amino Acidic Side Chain. Pharmaceuticals (Basel) 2024; 17:487. [PMID: 38675447 PMCID: PMC11054274 DOI: 10.3390/ph17040487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
We present a new category of quinoxaline di-N-oxides (QdNOs) containing amino acid side chains with dual antituberculosis and antileishmanial activity. These compounds were synthesized by combining a regioselective 2,5-piperazinedione opening and a Beirut reaction and were screened for their activity against Mycobacterium tuberculosis and the promastigote and amastigote forms of representative species of the Leishmania genus. Most QdNOs exhibited promising antitubercular activity with IC50 values ranging from 4.28 to 49.95 μM, comparable to clinically established drugs. Structure-activity relationship analysis emphasized the importance of substituents on the aromatic ring and the side chain. Antileishmanial tests showed that some selected compounds exhibited activity comparable to the positive control miltefosine against promastigotes of Leishmania amazonensis and Leishmania donovani. Notably, some compounds were found to be also more potent and less toxic than miltefosine in intracellular amastigote assays against Leishmania amazonensis. The compound showing the best dual antitubercular and leishmanicidal profile and a good selectivity index, 4h, can be regarded as a hit compound that opens up new opportunities for the development of integrated therapies against co-infections.
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Affiliation(s)
- Juan F. González
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain; (J.F.G.); (L.H.); (J.M.O.); (E.d.l.C.)
| | - María-Auxiliadora Dea-Ayuela
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, c/Santiago Ramón y Cajal, Alfara del Patriarca, 46115 Valencia, Spain;
| | - Lena Huck
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain; (J.F.G.); (L.H.); (J.M.O.); (E.d.l.C.)
| | - José María Orduña
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain; (J.F.G.); (L.H.); (J.M.O.); (E.d.l.C.)
| | - Francisco Bolás-Fernández
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain;
| | - Elena de la Cuesta
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain; (J.F.G.); (L.H.); (J.M.O.); (E.d.l.C.)
| | - Nazia Haseen
- AMIPRO SDN.BHD. Level 3, Bangunan Inkubator Universiti, Sains@USM, Lebuh Bukit Jambul, Bayan Lepas 11900, Pulau Pinang, Malaysia; (N.H.); (A.A.M.)
| | - Ashraf Ali Mohammed
- AMIPRO SDN.BHD. Level 3, Bangunan Inkubator Universiti, Sains@USM, Lebuh Bukit Jambul, Bayan Lepas 11900, Pulau Pinang, Malaysia; (N.H.); (A.A.M.)
| | - J. Carlos Menéndez
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain; (J.F.G.); (L.H.); (J.M.O.); (E.d.l.C.)
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12
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Díaz MA, Vega-Hissi EG, Blázquez MA, Alberto MR, Arena ME. Restraining Staphylococcus aureus Virulence Factors and Quorum Sensing through Lactic Acid Bacteria Supernatant Extracts. Antibiotics (Basel) 2024; 13:297. [PMID: 38666973 PMCID: PMC11047364 DOI: 10.3390/antibiotics13040297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/29/2024] Open
Abstract
The escalating prevalence of antibiotic-resistant bacteria poses a grave threat to human health, necessitating the exploration of novel alternatives to conventional antibiotics. This study investigated the impact of extracts derived from the supernatant of four lactic acid bacteria strains on factors contributing to the pathogenicity of three Staphylococcus aureus strains. The study evaluated the influence of lactic acid bacteria supernatant extracts on the growth, biofilm biomass formation, biofilm metabolic activity, and biofilm integrity of the S. aureus strains. Additionally, the impact on virulence factors (hemolysin and coagulase) was examined. Gas chromatography coupled with mass spectrometry was used to identify the bioactive compounds in the extracts, while molecular docking analyses explored potential interactions. Predominantly, the extracts contain eight 2,5-diketopiperazines, which are cyclic forms of peptides. The extracts demonstrated inhibitory effects on biofilm formation, the ability to disrupt mature biofilms, and reduce the biofilm cell metabolic activity of the S. aureus strains. Furthermore, they exhibited the ability to inhibit α-hemolysin production and reduce coagulase activity. An in silico docking analysis reveals promising interactions between 2,5-diketopiperazines and key proteins (SarA and AgrA) in S. aureus, confirming their antivirulence and antibiofilm activities. These findings suggest that 2,5-diketopiperazines could serve as a promising lead compound in the fight against antibiotic-resistant S. aureus.
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Affiliation(s)
- Myriam Anabel Díaz
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Chacabuco 461, San Miguel de Tucumán CP 4000, Argentina;
| | - Esteban Gabriel Vega-Hissi
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, San Luis CP 5700, Argentina;
| | - María Amparo Blázquez
- Departament de Farmacologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de València, Avd. Vicent Andrés Estellés s/n, Burjasot, 46100 Valencia, Spain
| | - María Rosa Alberto
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), Ayacucho 471, San Miguel de Tucumán CP 4000, Argentina
- Instituto de Biotecnología Farmacéutica y Alimentaria (INBIOFAL, CONICET-UNT), Avenida Kirchner 1900, San Miguel de Tucumán CP 4000, Argentina
| | - Mario Eduardo Arena
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), Ayacucho 471, San Miguel de Tucumán CP 4000, Argentina
- Instituto de Biotecnología Farmacéutica y Alimentaria (INBIOFAL, CONICET-UNT), Avenida Kirchner 1900, San Miguel de Tucumán CP 4000, Argentina
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13
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Liu X, Li K, Yu J, Ma C, Che Q, Zhu T, Li D, Pfeifer BA, Zhang G. Cyclo-diphenylalanine production in Aspergillus nidulans through stepwise metabolic engineering. Metab Eng 2024; 82:147-156. [PMID: 38382797 DOI: 10.1016/j.ymben.2024.02.009] [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: 11/28/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Cyclo-diphenylalanine (cFF) is a symmetrical aromatic diketopiperazine (DKP) found wide-spread in microbes, plants, and resulting food products. As different bioactivities continue being discovered and relevant food and pharmaceutical applications gradually emerge for cFF, there is a growing need for establishing convenient and efficient methods to access this type of compound. Here, we present a robust cFF production system which entailed stepwise engineering of the filamentous fungal strain Aspergillus nidulans A1145 as a heterologous expression host. We first established a preliminary cFF producing strain by introducing the heterologous nonribosomal peptide synthetase (NRPS) gene penP1 to A. nidulans A1145. Key metabolic pathways involving shikimate and aromatic amino acid biosynthetic support were then engineered through a combination of gene deletions of competitive pathway steps, over-expressing feedback-insensitive enzymes in phenylalanine biosynthesis, and introducing a phosphoketolase-based pathway, which diverted glycolytic flux toward the formation of erythrose 4-phosphate (E4P). Through the stepwise engineering of A. nidulans A1145 outlined above, involving both heterologous pathway addition and native pathway metabolic engineering, we were able to produce cFF with titers reaching 611 mg/L in shake flask culture and 2.5 g/L in bench-scale fed-batch bioreactor culture. Our study establishes a production platform for cFF biosynthesis and successfully demonstrates engineering of phenylalanine derived diketopiperazines in a filamentous fungal host.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Kang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jing Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, 14260, United States.
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China; Lab of Marine Medicinal Resources Discovery, Marine Biomedical Research Institute of Qingdao, Qingdao, 266075, China.
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14
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Zheng Y, Qin S, Xu L, Sang Z, Chen C, Tan J, Huang Y, Li M, Zou Z. Ochrolines A-C, three new indole diketopiperazines from cultures of endophytic fungi Bionectria ochroleuca SLJB-2. Fitoterapia 2024; 173:105809. [PMID: 38168565 DOI: 10.1016/j.fitote.2023.105809] [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: 10/15/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
Three new indole diketopiperazines, ochrolines A-C (1-3), along with three known compounds (4-6), were isolated and identified from the EtOAc extract of the solid fermentation of Bionectria ochroleuca SLJB-2. Notably, compound 1 featured a natural rarely-occurring caged skeleton with a 6/5/6/7 heterotetracyclic bridged ring system. The structures including absolute configurations of 1-3 were fully accomplished by extensive spectroscopic analyses, DFT GIAO 13C NMR and electronic circular dichroism (ECD) calculations. The plausible biogenetic pathways of these new indole diketopiperazines were also proposed. Moreover, the cytotoxic activity screening revealed that compound 2 exhibited moderate inhibitory effect against A549 with inhibition rate of 57.44% at the concentration of 50 μM and compound 1 exhibited mild inhibitory activities against A549, Hela and MCF-7.
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Affiliation(s)
- Yuting Zheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Siyu Qin
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Li Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Zihuan Sang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Chen Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Jianbing Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Yuantao Huang
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou 570100, China
| | - Meifang Li
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou 570100, China
| | - Zhenxing Zou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China.
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15
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Kang SO, Kwak MK. Antimicrobial Cyclic Dipeptides from Japanese Quail ( Coturnix japonica) Eggs Supplemented with Probiotic Lactobacillus plantarum. J Microbiol Biotechnol 2024; 34:314-329. [PMID: 38111307 PMCID: PMC10940788 DOI: 10.4014/jmb.2311.11006] [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: 11/07/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
Fifteen cyclic dipeptides (CDPs) containing proline, one cyclo(Phe-Ala) without proline, and a non-peptidyl DL-3-phenyllactic acid were previously identified in the culture filtrates of Lactobacillus plantarum LBP-K10, an isolate from kimchi. In this study, we used Japanese quail (Coturnix japonica) eggs to examine the effects of probiotic supplementation on the antimicrobial CDPs extracted from quail eggs (QE). Eggshell-free QE were obtained from two distinct groups of quails. The first group (K10N) comprised eggs from unsupplemented quails. The second group (K10S) comprised eggs from quails supplemented with Lb. plantarum LBP-K10. The QE samples were extracted using methylene chloride through a liquid-liquid extraction process. The resulting extract was fractionated into 16 parts using semi-preparative high-performance liquid chromatography. Two fractions, Q6 and Q9, were isolated from K10S and identified as cis-cyclo(L-Ser-L-Pro) and cis-cyclo(L-Leu-L-Pro). The Q9 fraction, containing cis-cyclo(L-Leu-L-Pro), has shown significant inhibitory properties against the proliferation of highly pathogenic multidrug-resistant bacteria, as well as human-specific and phytopathogenic fungi. Some of the ten combinations between the remaining fourteen unidentified fractions and two fractions, Q6 and Q9, containing cis-cyclo(L-Ser-L-Pro) and cis-cyclo(L-Leu-L-Pro) respectively, demonstrated a significant increase in activity against multidrug-resistant bacteria only when combined with Q9. The activity was 7.17 times higher compared to a single cis-cyclo(L-Leu-L-Pro). This study presents new findings on the efficacy of proline-containing CDPs in avian eggs. These CDPs provide antimicrobial properties when specific probiotics are supplemented.
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Affiliation(s)
- Sa-Ouk Kang
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of Korea
| | - Min-Kyu Kwak
- Laboratory of Microbial Physiology and Biotechnology, Department of Food and Nutrition, College of Bio-Convergence, and Institute of Food and Nutrition Science, Eulji University, Seongnam 13135, Republic of Korea
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16
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Ceravolo IP, Leoni LF, Krettli AU, Murta SMF, Resende DDM, Cruz MGFDML, Varejão JOS, Mendes LL, Varejão EVV, Kohlhoff M. Novel 2,5-Diketopiperazines with In Vitro Activities against Protozoan Parasites of Tropical Diseases. Pharmaceuticals (Basel) 2024; 17:223. [PMID: 38399438 PMCID: PMC10893061 DOI: 10.3390/ph17020223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 02/25/2024] Open
Abstract
Malaria, Chagas disease, and leishmaniasis are tropical diseases caused by protozoan parasites of the genera Plasmodium, Trypanosoma and Leishmania, respectively. These diseases constitute a major burden on public health in several regions worldwide, mainly affecting low-income populations in economically poor countries. Severe side effects of currently available drug treatments and the emergence of resistant parasites need to be addressed by the development of novel drug candidates. Natural 2,5-Diketopiperazines (2,5-DKPs) constitute N-heterocyclic secondary metabolites with a wide range of biological activities of medicinal interest. Its structural and physicochemical properties make the 2,5-DKP ring a versatile, peptide-like, and stable pharmacophore attractive for synthetic drug design. In the present work, twenty-three novel synthetic 2,5-DKPs, previously synthesized through the versatile Ugi multicomponent reaction, were assayed for their anti-protozoal activities against P. falciparum, T. cruzi, and L. infantum. Some of the 2,5-DKPs have shown promising activities against the target protozoans, with inhibitory concentrations (IC50) ranging from 5.4 to 9.5 µg/mL. The most active compounds also show low cytotoxicity (CC50), affording selectivity indices ≥ 15. Results allowed for observing a clear relationship between the substitution pattern at the aromatic rings of the 2,5-DKPs and their corresponding anti-Plasmodium activity. Finally, calculated drug-like properties of the compounds revealed points for further structure optimization of promising drug candidates.
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Affiliation(s)
- Isabela P. Ceravolo
- Laboratory of Immunopathology, René Rachou Institute (IRR), Oswaldo Cruz Foundation (FIOCRUZ), Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, Brazil; (I.P.C.); (L.F.L.); (A.U.K.)
| | - Letícia F. Leoni
- Laboratory of Immunopathology, René Rachou Institute (IRR), Oswaldo Cruz Foundation (FIOCRUZ), Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, Brazil; (I.P.C.); (L.F.L.); (A.U.K.)
| | - Antoniana U. Krettli
- Laboratory of Immunopathology, René Rachou Institute (IRR), Oswaldo Cruz Foundation (FIOCRUZ), Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, Brazil; (I.P.C.); (L.F.L.); (A.U.K.)
| | - Silvane M. F. Murta
- Laboratory of Functional Genomics of Parasites, René Rachou Institute (IRR), Oswaldo Cruz Foundation (FIOCRUZ), Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, Brazil; (S.M.F.M.); (D.d.M.R.); (M.G.F.d.M.L.C.)
| | - Daniela de M. Resende
- Laboratory of Functional Genomics of Parasites, René Rachou Institute (IRR), Oswaldo Cruz Foundation (FIOCRUZ), Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, Brazil; (S.M.F.M.); (D.d.M.R.); (M.G.F.d.M.L.C.)
| | - Mariza G. F. de M. L. Cruz
- Laboratory of Functional Genomics of Parasites, René Rachou Institute (IRR), Oswaldo Cruz Foundation (FIOCRUZ), Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, Brazil; (S.M.F.M.); (D.d.M.R.); (M.G.F.d.M.L.C.)
| | - Jodieh O. S. Varejão
- Laboratory of Natural Product Chemistry Studies and Organic Synthesis, Federal University of Viçosa (UFV), Av. PH Rolfs, s/n, Viçosa 36570-900, Brazil; (J.O.S.V.); (L.L.M.); (E.V.V.V.)
| | - Lorena L. Mendes
- Laboratory of Natural Product Chemistry Studies and Organic Synthesis, Federal University of Viçosa (UFV), Av. PH Rolfs, s/n, Viçosa 36570-900, Brazil; (J.O.S.V.); (L.L.M.); (E.V.V.V.)
| | - Eduardo V. V. Varejão
- Laboratory of Natural Product Chemistry Studies and Organic Synthesis, Federal University of Viçosa (UFV), Av. PH Rolfs, s/n, Viçosa 36570-900, Brazil; (J.O.S.V.); (L.L.M.); (E.V.V.V.)
| | - Markus Kohlhoff
- Laboratory of Bioactive Natural Product Chemistry, René Rachou Institute (IRR), Oswaldo Cruz Foundation (FIOCRUZ), Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, Brazil
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17
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Zhang YH, Du HF, Liu YF, Cao F, Luo DQ, Wang CY. Novel anti-inflammatory diketopiperazine alkaloids from the marine-derived fungus Penicillium brasilianum. Appl Microbiol Biotechnol 2024; 108:194. [PMID: 38315417 PMCID: PMC10844341 DOI: 10.1007/s00253-024-13026-4] [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: 08/25/2023] [Revised: 12/30/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
Diketopiperazine alkaloids have proven the most abundant heterocyclic alkaloids up to now, which usually process diverse scaffolds and rich biological activities. In our search for bioactive diketopiperazine alkaloids from marine-derived fungi, two novel diketopiperazine alkaloids, penipiperazine A (1) and its biogenetically related new metabolite (2), together with a known analogue neofipiperzine C (3), were obtained from the strain Penicillium brasilianum. Their planar structures and absolute configurations were elucidated by extensive spectroscopic analyses, 13C NMR calculation, Marfey's, ECD, and ORD methods. Compound 1 featured a unique 6/5/6/6/5 indole-pyrazino-pyrazino-pyrrolo system, and its plausible biogenetic pathway was also proposed. Additionally, compounds 1-3 have been tested for their inflammatory activities. 1 and 2 significantly inhibited the release of NO and the expression of related pro-inflammatory cytokines on LPS-stimulated RAW264.7 cells, suggesting they could be attracting candidate for further development as anti-inflammatory agent. KEY POINTS: • A novel diketopiperazine alkaloid featuring a unique 6/5/6/6/5 indole-pyrazino-pyrazino-pyrrolo system was isolated from the marine fungus Penicillium brasilianum. • The structure of 1 was elucidated by detailed analysis of 2D NMR data, 13C NMR calculation, Marfey's, ECD, and ORD methods. • Compounds 1 and 2 significantly inhibited the release of NO and the expression of related pro-inflammatory cytokines on LPS-stimulated RAW264.7 cells.
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Affiliation(s)
- Ya-Hui Zhang
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China
| | - Hui-Fang Du
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yun-Feng Liu
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China
| | - Fei Cao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China.
| | - Du-Qiang Luo
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China.
| | - Chang-Yun Wang
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, the Ministry of Education of China, School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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18
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Liu Z, Sun W, Hu Z, Wang W, Zhang H. Marine Streptomyces-Derived Novel Alkaloids Discovered in the Past Decade. Mar Drugs 2024; 22:51. [PMID: 38276653 PMCID: PMC10821133 DOI: 10.3390/md22010051] [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: 12/18/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/27/2024] Open
Abstract
Natural alkaloids originating from actinomycetes and synthetic derivatives have always been among the important suppliers of small-molecule drugs. Among their biological sources, Streptomyces is the highest and most extensively researched genus. Marine-derived Streptomyces strains harbor unconventional metabolic pathways and have been demonstrated to be efficient producers of biologically active alkaloids; more than 60% of these compounds exhibit valuable activity such as antibacterial, antitumor, anti-inflammatory activities. This review comprehensively summarizes novel alkaloids produced by marine Streptomyces discovered in the past decade, focusing on their structural features, biological activity, and pharmacological mechanisms. Future perspectives on the discovery and development of novel alkaloids from marine Streptomyces are also provided.
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Affiliation(s)
| | | | | | | | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (Z.L.); (W.S.); (Z.H.); (W.W.)
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19
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Tasdemir D, Scarpato S, Utermann-Thüsing C, Jensen T, Blümel M, Wenzel-Storjohann A, Welsch C, Echelmeyer VA. Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168422. [PMID: 37956849 DOI: 10.1016/j.scitotenv.2023.168422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Seagrass meadows provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of waterborne pathogens linked to infections in humans and marine organisms in their vicinity. Among potential drivers, seagrass phenolics released into seawater have been linked to pathogen suppression, but the potential involvement of the seagrass microbiome has not been investigated. We hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and the surrounding seawater, inhibit waterborne pathogens thereby contributing to their removal. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots. We assessed the antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and mined the metabolome of the most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also displayed remarkable activities. UPLC-MS/MS-based untargeted metabolomics analyses showed rich specialized metabolite repertoires with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome in suppression of pathogens in seawater. Such effect is beneficial for the health of ocean and human, especially in the context of climate change that is expected to exacerbate all infectious diseases. It may also assist future seagrass conservation and management strategies.
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Affiliation(s)
- Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany; Faculty of Mathematics and Natural Sciences, Kiel University, Kiel 24118, Germany.
| | - Silvia Scarpato
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Caroline Utermann-Thüsing
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Timo Jensen
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Arlette Wenzel-Storjohann
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Claudia Welsch
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
| | - Vivien Anne Echelmeyer
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24106, Germany
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20
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Freimoser FM, Mahler M, McCullough M, Brachmann AO, Nägeli L, Hilber-Bodmer M, Piel J, Hoffmann SA, Cai Y. Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation. FEMS Yeast Res 2024; 24:foad053. [PMID: 38140959 PMCID: PMC10786192 DOI: 10.1093/femsyr/foad053] [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: 08/08/2023] [Revised: 12/01/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023] Open
Abstract
Pulcherrimin is an iron (III) chelate of pulcherriminic acid that plays a role in antagonistic microbial interactions, iron metabolism, and stress responses. Some bacteria and yeasts produce pulcherriminic acid, but so far, pulcherrimin could not be produced in Saccharomyces cerevisiae. Here, multiple integrations of the Metschnikowia pulcherrima PUL1 and PUL2 genes in the S. cerevisiae genome resulted in red colonies, which indicated pulcherrimin formation. The coloration correlated positively and significantly with the number of PUL1 and PUL2 genes. The presence of pulcherriminic acid was confirmed by mass spectrometry. In vitro competition assays with the plant pathogenic fungus Botrytis caroliana revealed inhibitory activity on conidiation by an engineered, strong pulcherrimin-producing S. cerevisiae strain. We demonstrate that the PUL1 and PUL2 genes from M. pulcherrima, in multiple copies, are sufficient to transfer pulcherrimin production to S. cerevisiae and represent the starting point for engineering and optimizing this biosynthetic pathway in the future.
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Affiliation(s)
- Florian M Freimoser
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Marina Mahler
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Mark McCullough
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester M1 7DN, UK
| | - Alexander O Brachmann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Lukas Nägeli
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Maja Hilber-Bodmer
- Agroscope, Research Division Plant Protection, Route de Duillier 60, 1260 Nyon 1, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester M1 7DN, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester M1 7DN, UK
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21
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Haase M, David B, Paschold B, Classen T, Schneider P, Pozhydaieva N, Gohlke H, Pietruszka J. Application of the C3-Methyltransferase StspM1 for the Synthesis of the Natural Pyrroloindole Motif. ACS Catal 2024; 14:227-236. [PMID: 38205025 PMCID: PMC10775177 DOI: 10.1021/acscatal.3c04952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
Even though pyrroloindoles are widely present in natural products with different kinds of biological activities, their selective synthesis remains challenging with existing tools in organic chemistry, and there is furthermore a demand for stereoselective and mild methods to access this structural motif. Nature uses C3-methyltransferases to form the pyrroloindole framework, starting from the amino acid tryptophan. In the present study, the SAM-dependent methyltransferase StspM1 from Streptomyces sp. HPH0547 is used to build the pyrroloindole structural motif in tryptophan-based diketopiperazines (DKP). The substrate scope of the enzyme regarding different Trp-Trp-DKP isomers was investigated on an experimental and computational level. After further characterization and optimization of the methylation reaction with a design of experiment approach, a preparative scale reaction with the immobilized enzyme including a SAM regeneration system was performed to show the synthetic use of this biocatalytic tool to access the pyrroloindole structural motif.
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Affiliation(s)
- Mona Haase
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Benoit David
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics) Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Beatrix Paschold
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Thomas Classen
- Institute
of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy
Science Center (BioSC), Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Pascal Schneider
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Nadiia Pozhydaieva
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
| | - Holger Gohlke
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics) Forschungszentrum
Jülich, 52426 Jülich, Germany
- Institute
for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science
Center (BioSC), Heinrich Heine University
Düsseldorf, 40225 Düsseldorf, Germany
| | - Jörg Pietruszka
- Institute
for Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum
Jülich, 52426 Jülich, Germany
- Institute
of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy
Science Center (BioSC), Forschungszentrum
Jülich, 52426 Jülich, Germany
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22
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Goher SS, Abdrabo WS, Veerakanellore GB, Elgendy B. 2,5-Diketopiperazines (DKPs): Promising Scaffolds for Anticancer Agents. Curr Pharm Des 2024; 30:597-623. [PMID: 38343054 DOI: 10.2174/0113816128291798240201112916] [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: 11/07/2023] [Accepted: 01/22/2024] [Indexed: 05/25/2024]
Abstract
2,5-Diketopiperazine (2,5-DKP) derivatives represent a family of secondary metabolites widely produced by bacteria, fungi, plants, animals, and marine organisms. Many natural products with DKP scaffolds exhibited various pharmacological activities such as antiviral, antifungal, antibacterial, and antitumor. 2,5-DKPs are recognized as privileged structures in medicinal chemistry, and compounds that incorporate the 2,5-DKP scaffold have been extensively investigated for their anticancer properties. This review is a thorough update on the anti-cancer activity of natural and synthesized 2,5-DKPs from 1997 to 2022. We have explored various aspects of 2,5-DKPs modifications and summarized their structure-activity relationships (SARs) to gain insight into their anticancer activities. We have also highlighted the novel approaches to enhance the specificity and pharmacokinetics of 2,5-DKP-based anticancer agents.
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Affiliation(s)
- Shaimaa S Goher
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
- Nanotechnology Research Centre (NTRC), The British University in Egypt (BUE), Suez Desert Road, El Sherouk City, Cairo 1183, Egypt
| | - Wessam S Abdrabo
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Giri Babu Veerakanellore
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, St. Louis, Missouri 63110, United States
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
| | - Bahaa Elgendy
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, St. Louis, Missouri 63110, United States
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
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23
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Maujean T, Kannaboina P, Green AI, Burslem GM. Lead-oriented synthesis of epigenetic relevant scaffolds. Chem Commun (Camb) 2023; 59:14555-14558. [PMID: 37991354 PMCID: PMC10842704 DOI: 10.1039/d3cc04317g] [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] [Indexed: 11/23/2023]
Abstract
A simple and rational method to rank lead-likeness of molecules using continuous evaluation functions was hereby developed. This strategy proved to be competitive against known methods and finally helped in driving synthetic efforts towards candidates of interest for epigenetic applications against HDAC6, BRD4 and EZH2.
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Affiliation(s)
- Timothé Maujean
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
| | - Prakash Kannaboina
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
| | - Adam I Green
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
| | - George M Burslem
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
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24
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Großkopf J, Plaza M, Kutta RJ, Nuernberger P, Bach T. Creating a Defined Chirality in Amino Acids and Cyclic Dipeptides by Photochemical Deracemization. Angew Chem Int Ed Engl 2023; 62:e202313606. [PMID: 37793026 DOI: 10.1002/anie.202313606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023]
Abstract
2,5-Diketopiperazines are cyclic dipeptides displaying a wide range of applications. Their enantioselective preparation has now been found possible from the respective racemates by a photochemical deracemization (53 examples, 74 % to quantitative yield, 71-99 % ee). A chiral benzophenone catalyst in concert with irradiation at λ=366 nm enables to establish the configuration at the stereogenic carbon atom C6 at will. If other stereogenic centers are present in the diketopiperazines they remain unaffected and a stereochemical editing is possible at a single position. Consecutive reactions, including the conversion into N-aryl or N-alkyl amino acids or the reduction to piperazines, occur without compromising the newly created stereogenic center. Transient absorption spectroscopy revealed that the benzophenone catalyst processes one enantiomer of the 2,5-diketopiperazines preferentially and enables a reversible hydrogen atom transfer that is responsible for the deracemization process. The remarkably long lifetime of the protonated ketyl radical implies a yet unprecedented mode of action.
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Affiliation(s)
- Johannes Großkopf
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747, Garching, Germany
| | - Manuel Plaza
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747, Garching, Germany
| | - Roger Jan Kutta
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747, Garching, Germany
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25
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Fang W, Sun BB, Qin SC, Fang LP, Yu XR, Jiang HJ, Yu J. Enantioselective Access to Chiral 2,5-Diketopiperazines via Stereogenic-at-Cobalt(III)-Catalyzed Ugi-4CRs/Cyclization Sequences. J Org Chem 2023; 88:16024-16037. [PMID: 37917565 DOI: 10.1021/acs.joc.3c02013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
An asymmetric synthesis of chiral 2,5-diketopiperazines by the Ugi-4CR/cyclization is exhibited. The employment of catalytic anionic chiral Co(III) complexes delivered α-propiolyl aminoamides in high yields with excellent enantioselectivities (31 examples, up to 95% ee). The following treatment of Ugi-adducts with PPh3 leads to chiral 2,5-DKPs without significant loss of enantioselectivities (26 examples, up to 91% ee).
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Affiliation(s)
- Wei Fang
- Department of Applied Chemistry, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, and Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Bing-Bing Sun
- Department of Applied Chemistry, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, and Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Shi-Cheng Qin
- Department of Applied Chemistry, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, and Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Li-Ping Fang
- Department of Applied Chemistry, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, and Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Xin-Ran Yu
- Department of Applied Chemistry, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, and Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Hua-Jie Jiang
- Department of Applied Chemistry, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, and Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Jie Yu
- Department of Applied Chemistry, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, and Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, P. R. China
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26
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Gholami H, Cornali BM. Diastereoselective Spirocyclization: Entry to Spirocyclic Diketopiperazines. Org Lett 2023; 25:7822-7826. [PMID: 37857286 DOI: 10.1021/acs.orglett.3c03031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
We report a novel approach to access spirocyclic compounds containing a diketopiperazine (DKP) motif fused on a pyrrolidine ring. The shared spirocyclic carbon is at the ketone oxidation state, bearing two carbon-nitrogen bonds, one of which is introduced stereoselectively during the cyclization event. The reaction proceeds through an acid-catalyzed cyclization of a pendent chiral aminoamide unit onto a 2,3-dehydroproline amide moiety with up to >98:2 diastereoselectivity. We have demonstrated the generality of this methodology and its applicability to access chemically diverse DKP-containing structures. The extent of stereoinduction and how it varies according to the bulkiness of the substituent on the pendent aminoamide is demonstrated through a diverse substrate set. This methodology gives access to an underexplored spirocyclic diketopiperazine motif that may be useful in identifying new bioactive molecules.
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Affiliation(s)
- Hadi Gholami
- Janssen Research and Development, 3210 Merryfield Row, San Diego, California 92121, United States
| | - Brandon M Cornali
- Janssen Research and Development, 3210 Merryfield Row, San Diego, California 92121, United States
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27
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Singh C, Sharma P, Ahmed M, Kumar D, Sharma YB, Samanta J, Ahmed Z, Shukla SK, Hazra A, Bharitkar YP. Semisynthesis of Novel Dispiro-pyrrolizidino/thiopyrrolizidino-oxindolo/indanedione Natural Product Hybrids of Parthenin Followed by Their Cytotoxicity Evaluation. ACS OMEGA 2023; 8:35283-35294. [PMID: 37779957 PMCID: PMC10536096 DOI: 10.1021/acsomega.3c05020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Natural products possess unique and broader intricacies in the chemical space and have been essential for drug discovery. The crucial factor for drug discovery success is not the size of the library but rather its structural diversity. Although reports on the number of new structurally diverse natural products (NPs) have declined recently, researchers follow the next logical step: synthesizing natural product hybrids and their analogues using the most potent tool, diversity-oriented synthesis (DOS). Here, we use weed Parthenium hysterophorus as a source of parthenin for synthesis of novel dispiro-pyrrolizidino/thiopyrrolizidino-oxindolo/indanedione natural product hybrids of parthenin via chemo-, regio-, and stereoselective azomethine ylide cycloaddition. All synthesized compounds were characterized through a detailed analysis of one-dimensional (1D) and two-dimensional (2D) NMR and HRMS data, and the stereochemistries of the compounds were confirmed by X-ray diffraction analysis. All compounds were evaluated for their cytotoxicity against four cell lines (HCT-116, A549, Mia-Paca-2, and MCF-7), and compound 6 inhibited the HCT-116 cells with an IC50 of 5.0 ± 0.08 μM.
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Affiliation(s)
- Chetan
Paul Singh
- CSIR-Indian
Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priyanka Sharma
- National
Institute of Pharmaceutical Education and Research (NIPER), Chunilal Bhawan, 168, Maniktala
Main Road, Kolkata 700054, India
| | - Manzoor Ahmed
- CSIR-Indian
Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Diljeet Kumar
- CSIR-Indian
Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Yogesh Brijwashi Sharma
- National
Institute of Pharmaceutical Education and Research (NIPER), Chunilal Bhawan, 168, Maniktala
Main Road, Kolkata 700054, India
| | - Jayanta Samanta
- Department
of Chemistry, SRM Institute of Science and
Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Zabeer Ahmed
- CSIR-Indian
Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sanket Kumar Shukla
- CSIR-Indian
Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abhijit Hazra
- National
Institute of Pharmaceutical Education and Research (NIPER), Chunilal Bhawan, 168, Maniktala
Main Road, Kolkata 700054, India
| | - Yogesh P. Bharitkar
- CSIR-Indian
Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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28
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Andreas MP, Giessen TW. Cyclodipeptide oxidase is an enzyme filament. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559410. [PMID: 37808672 PMCID: PMC10557607 DOI: 10.1101/2023.09.25.559410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that all CDO-like enzymes are likely enzyme filaments. Our work represents the first structural characterization of a CDO. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
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Affiliation(s)
- Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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29
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Chen CM, Yang YN, Kong YZ, Zhu BH, Qian PC, Zhou B, Ye LW. Copper-catalyzed intermolecular formal (5 + 1) annulation of 1,5-diynes with 1,2,5-oxadiazoles. Commun Chem 2023; 6:194. [PMID: 37700020 PMCID: PMC10497616 DOI: 10.1038/s42004-023-00999-y] [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: 06/13/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
One-carbon homologation reactions based on one-carbon insertion into the N-O bond of heterocycles have received tremendous interest over the past decades. However, these protocols have to rely on the use of hazardous and not easily accessible diazo compounds as precursors, and examples of the relevant asymmetric catalysis have not been reported. Here we show that a copper-catalyzed intermolecular formal (5 + 1) annulation of 1,5-diynes with 1,2,5-oxadiazoles involving one-carbon insertion into the heterocyclic N-O bond via non-diazo approach. This method enables practical and atom-economic synthesis of valuable pyrrole-substituted oxadiazines in generally moderate to good yields under mild reaction conditions. In addition, the possibility of such an asymmetric formal (5 + 1) annulation also emerges.
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Affiliation(s)
- Can-Ming Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Ye-Nan Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yin-Zhu Kong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Bo-Han Zhu
- College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou, China
| | - Peng-Cheng Qian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
- College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou, China.
- Wenzhou Key Laboratory of Technology and Application of Environmental Functional Materials, Institute of New Materials & Industry Technology, Wenzhou University, Wenzhou, China.
| | - Bo Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Long-Wu Ye
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
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30
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Gering HE, Li X, Tang H, Swartz PD, Chang WC, Makris TM. A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization. J Am Chem Soc 2023; 145:19256-19264. [PMID: 37611404 DOI: 10.1021/jacs.3c04542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The cytochrome P450 (CYP) AspB is involved in the biosynthesis of the diketopiperazine (DKP) aspergilazine A. Tryptophan-linked dimeric DKP alkaloids are a large family of natural products that are found in numerous species and exhibit broad and often potent bioactivity. The proposed mechanisms for C-N bond formation by AspB, and similar C-C bond formations by related CYPs, have invoked the use of a ferryl-intermediate as an oxidant to promote substrate dimerization. Here, the parallel application of steady-state and transient kinetic approaches reveals a very different mechanism that involves a ferric-superoxide species as a primary oxidant to initiate DKP-assembly. Single turnover kinetic isotope effects and a substrate analog suggest the probable nature and site for abstraction. The direct observation of CYP-superoxide reactivity rationalizes the atypical outcome of AspB and reveals a new reaction manifold in heme enzymes.
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Affiliation(s)
- Hannah E Gering
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Haoyu Tang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul D Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas M Makris
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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31
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Kurita D, Sato H, Miyamoto K, Uchiyama M. Mechanistic Investigation of the Degradation Pathways of α-β/α-α Bridged Epipolythiodioxopiperazines (ETPs). J Org Chem 2023; 88:12797-12801. [PMID: 37574909 DOI: 10.1021/acs.joc.3c01061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Epipolythiodioxopiperazines (ETPs) make up a class of biologically active fungal metabolites with a transannular disulfide bridge. In this work, we used DFT calculations to examine in detail the degradation (desulfurization) pathways of α-β/α-α bridged ETPs. The chemical stability of ETPs is influenced by the type of sulfur bridge, the structural features, and the storage conditions. Our results suggest appropriate protection of the phenolic OH of ETPs would improve various pharmaceutically relevant properties, including bioavailability.
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Affiliation(s)
- Daiki Kurita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hajime Sato
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research Initiative for Supra-Materials (RISM), Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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32
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Deigin V, Linkova N, Volpina O. Advancement from Small Peptide Pharmaceuticals to Orally Active Piperazine-2,5-dion-Based Cyclopeptides. Int J Mol Sci 2023; 24:13534. [PMID: 37686336 PMCID: PMC10487935 DOI: 10.3390/ijms241713534] [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: 07/22/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The oral delivery of peptide pharmaceuticals has long been a fundamental challenge in drug development. A new chemical platform was designed based on branched piperazine-2,5-diones for creating orally available biologically active peptidomimetics. The platform includes a bio-carrier with "built-in" functionally active peptide fragments or bioactive molecules that are covalently attached via linkers. The developed platform allows for a small peptide to be taken with a particular biological activity and to be transformed into an orally stable compound displaying the same activity. Based on this approach, various peptidomimetics exhibiting hemostimulating, hemosuppressing, and adjuvant activity were prepared. In addition, new examples of a rare phenomenon when enantiomeric molecules demonstrate reciprocal biological activity are presented. Finally, the review summarizes the evolutionary approach of the short peptide pharmaceutical development from the immunocompetent organ separation to orally active cyclopeptides and peptidomimetics.
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Affiliation(s)
- Vladislav Deigin
- The Laboratory of Synthetic Vaccines of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia;
| | - Natalia Linkova
- The Research Laboratory of the Development of Drug Delivery Systems, St. Petersburg Research Institute of Phthisiopulmonology, Ligovskii Prospect, 2-4, St. Petersburg 191036, Russia;
| | - Olga Volpina
- The Laboratory of Synthetic Vaccines of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia;
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33
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Perumal K, Lee J, Annes SB, Ramesh S, Rangarajan TM, Mathew B, Kim H. An efficient method to access spiro pseudoindoxyl ketones: evaluation of indoxyl and their N-benzylated derivatives for inhibition of the activity of monoamine oxidases. RSC Adv 2023; 13:24925-24935. [PMID: 37614797 PMCID: PMC10442599 DOI: 10.1039/d3ra03641c] [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: 05/31/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023] Open
Abstract
A simple, metal-free approach was developed to obtain novel pseudoindoxyl derivatives. The reaction was mediated by tBuOK on tetrahydrocarbazole 8 in dimethyl sulfoxide (DMSO) at room temperature through the hydroxylation of the indole double bond and a subsequent pinacol-type rearrangement. Spiro pseudoindoxyl compounds and their N-benzylated derivatives were assessed for their inhibitory activities against monoamine oxidase (MAO) enzymes. Based on half-maximal inhibitory concentration (IC50) values, 13 compounds were found to have higher inhibitory activity against MAO-B than against MAO-A. With regard to MAO-B inhibition, 11f showed the best inhibitory activity, with an IC50 value of 1.44 μM, followed by 11h (IC50 = 1.60 μM), 11j (IC50 = 2.78 μM), 11d (IC50 = 2.81 μM), and 11i (IC50 = 3.02 μM). Compound 11f was a competitive inhibitor with a Ki value of 0.51 ± 0.023 μM. In a reversibility experiment using dialysis, 11f showed effective recovery of MAO-B inhibition similar to that of safinamide. These experiments suggested that 11f was a potent, reversible, and competitive inhibitor of MAO-B activity.
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Affiliation(s)
- Karuppaiah Perumal
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Jiseong Lee
- Department of Pharmacy, Research Institute of Life Pharmaceutical Sciences, Sunchon National University Suncheon 57922 Republic of Korea
| | - Sesuraj Babiola Annes
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Subburethinam Ramesh
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - T M Rangarajan
- Department of Chemistry, Sri Venkateswara College, University of Delhi New Delhi India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus Kochi 682 041 India
| | - Hoon Kim
- Department of Pharmacy, Research Institute of Life Pharmaceutical Sciences, Sunchon National University Suncheon 57922 Republic of Korea
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34
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Walker KL, Loach RP, Movassaghi M. Total synthesis of complex 2,5-diketopiperazine alkaloids. THE ALKALOIDS. CHEMISTRY AND BIOLOGY 2023; 90:159-206. [PMID: 37716796 PMCID: PMC10955524 DOI: 10.1016/bs.alkal.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
The 2,5-diketopiperazine (DKP) motif is present in many biologically relevant, complex natural products. The cyclodipeptide substructure offers structural rigidity and stability to proteolysis that makes these compounds promising candidates for medical applications. Due to their fascinating molecular architecture, synthetic organic chemists have focused significant effort on the total synthesis of these compounds. This review covers many such efforts on the total synthesis of DKP containing complex alkaloid natural products.
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Affiliation(s)
- Katherine L Walker
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Richard P Loach
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Mohammad Movassaghi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States.
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Witkowski M, Trzybiński D, Pawlędzio S, Woźniak K, Dzwolak W, Królikowska A. The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State. Molecules 2023; 28:5902. [PMID: 37570871 PMCID: PMC10421304 DOI: 10.3390/molecules28155902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the P-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.
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Affiliation(s)
- Marcin Witkowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Agata Królikowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
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36
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Stierle SA, Harken L, Li SM. Production of Diketopiperazine Derivatives by Pathway Engineering with Different Cyclodipeptide Synthases from Various Streptomyces Strains. ACS Synth Biol 2023; 12:1804-1812. [PMID: 37183364 DOI: 10.1021/acssynbio.3c00115] [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] [Indexed: 05/16/2023]
Abstract
Cyclodipeptides from fungi and bacteria are often modified by different tailoring enzymes. They display various biological and pharmacological activities, and some derivatives are used as drugs. In a previous study, we elucidated the function of the silent guatrypmethine gene cluster from Streptomyces cinnamoneus containing a cyclodipeptide synthase (CDPS) core gene gtmA and four genes gtmB-gtmE for tailoring enzymes. The latter are used in this study for the design of modified cyclodipeptides by genetic engineering. Addition of six different cyclodipeptides to the Streptomyces albus transformant harboring gtmB-gtmE led to the detection of different pathway products. Coexpression of five CDPS genes from four Streptomyces strains with gtmB-gtmE resulted in the formation of diketopiperazine derivatives, differing in their modification stages. Our results demonstrate the potential of rational gene combination to increase structural diversity.
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Affiliation(s)
- Sina A Stierle
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, 35037 Marburg, Germany
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37
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Ogilvie CE, Czekster CM. Cyclic dipeptides and the human microbiome: Opportunities and challenges. Bioorg Med Chem 2023; 90:117372. [PMID: 37343497 DOI: 10.1016/j.bmc.2023.117372] [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: 04/08/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
Research into the human microbiome has implicated its constituents in a variety of non-communicable diseases, with certain microbes found to promote health and others leading to dysbiosis and pathogenesis.Microbes communicate and coordinate their behaviour through the secretion of small molecules, such as cyclic dipeptides (CDPs), into their surrounding environment. CDPs are ubiquitous signalling molecules thatexhibit a wide range of biological activities, with particular relevance to human health due to their potential to act as microbiome modulators.
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Affiliation(s)
- Charlene Elizabeth Ogilvie
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.
| | - Clarissa Melo Czekster
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.
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38
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Li X, Xun T, Xu H, Pang X, Yang B, Wang J, Zhou X, Lin X, Tan S, Liu Y, Liao S. Design, Synthesis, and Anticancer Activity of Novel 3,6-Diunsaturated 2,5-Diketopiperazines. Mar Drugs 2023; 21:325. [PMID: 37367651 DOI: 10.3390/md21060325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Based on the marine natural products piperafizine B, XR334, and our previously reported compound 4m, fourteen novel 3,6-diunsaturated 2,5-diketopiperazine (2,5-DKP) derivatives (1, 2, 4-6, 8-16), together with two known ones (3 and 7), were designed and synthesized as anticancer agents against the A549 and Hela cell lines. The MTT assay results showed that the derivatives 6, 8-12, and 14 had moderate to good anticancer capacities, with IC50 values ranging from 0.7 to 8.9 μM. Among them, compound 11, with naphthalen-1-ylmethylene and 2-methoxybenzylidene functions at the 3 and 6 positions of 2,5-DKP ring, respectively, displayed good inhibitory activities toward both A549 (IC50 = 1.2 μM) and Hela (IC50 = 0.7 μM) cancer cells. It could also induce apoptosis and obviously block cell cycle progression in the G2/M phases in both cells at 1.0 μM. The electron-withdrawing functions might not be favorable for the derivatives with high anticancer activities. Additionally, compared to piperafizine B and XR334, these semi-N-alkylated derivatives have high liposolubilities (>1.0 mg mL-1). Compound 11 can be further developed, aiming at the discovery of a novel anticancer candidate.
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Affiliation(s)
- Xiaolin Li
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianrong Xun
- Department of Pharmacy, Southern Medical University, Shenzhen 518100, China
| | - Huayan Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaoyan Pang
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Bin Yang
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junfeng Wang
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuefeng Zhou
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuping Lin
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Suiyi Tan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yonghong Liu
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shengrong Liao
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Shende VV, Harris NR, Sanders JN, Newmister SA, Khatri Y, Movassaghi M, Houk KN, Sherman DH. Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases. Angew Chem Int Ed Engl 2023; 62:e202210254. [PMID: 36610039 PMCID: PMC10159983 DOI: 10.1002/anie.202210254] [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: 07/13/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp2 -N bond forming dimerase, AspB. Overlay of the AspB structure onto C-C and C-N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C-N bond formation. MD simulations also suggest that intermolecular C-C or C-N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.
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Affiliation(s)
- Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Natalia R Harris
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Yogan Khatri
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Mohammad Movassaghi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
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40
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Deletti G, Green SD, Weber C, Patterson KN, Joshi SS, Khopade TM, Coban M, Veek-Wilson J, Caulfield TR, Viswanathan R, Lane AL. Unveiling an indole alkaloid diketopiperazine biosynthetic pathway that features a unique stereoisomerase and multifunctional methyltransferase. Nat Commun 2023; 14:2558. [PMID: 37137876 PMCID: PMC10156859 DOI: 10.1038/s41467-023-38168-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
The 2,5-diketopiperazines are a prominent class of bioactive molecules. The nocardioazines are actinomycete natural products that feature a pyrroloindoline diketopiperazine scaffold composed of two D-tryptophan residues functionalized by N- and C-methylation, prenylation, and diannulation. Here we identify and characterize the nocardioazine B biosynthetic pathway from marine Nocardiopsis sp. CMB-M0232 by using heterologous biotransformations, in vitro biochemical assays, and macromolecular modeling. Assembly of the cyclo-L-Trp-L-Trp diketopiperazine precursor is catalyzed by a cyclodipeptide synthase. A separate genomic locus encodes tailoring of this precursor and includes an aspartate/glutamate racemase homolog as an unusual D/L isomerase acting upon diketopiperazine substrates, a phytoene synthase-like prenyltransferase as the catalyst of indole alkaloid diketopiperazine prenylation, and a rare dual function methyltransferase as the catalyst of both N- and C-methylation as the final steps of nocardioazine B biosynthesis. The biosynthetic paradigms revealed herein showcase Nature's molecular ingenuity and lay the foundation for diketopiperazine diversification via biocatalytic approaches.
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Affiliation(s)
- Garrett Deletti
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Sajan D Green
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Caleb Weber
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Kristen N Patterson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Swapnil S Joshi
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Tushar M Khopade
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - James Veek-Wilson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Thomas R Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rajesh Viswanathan
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India.
| | - Amy L Lane
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
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41
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Koshizuka M, Shinoda K, Makino K, Shimada N. Concise Synthesis of 2,5-Diketopiperazines via Catalytic Hydroxy-Directed Peptide Bond Formations. J Org Chem 2023. [PMID: 37125993 DOI: 10.1021/acs.joc.3c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
2,5-Diketopiperazines (DKPs) with hydroxymethyl functional groups are essential structures found in many bioactive molecules and functional materials. We have established a simple protocol for the concise synthesis of this type of DKPs through diboronic acid anhydride-catalyzed hydroxy-directed peptide bond formations. The sequential reactions in this report, which consist of three steps, an intermolecular catalytic condensation reaction in which water is the only byproduct, a simple deprotection of the nitrogen-protecting group, and an intramolecular cyclization, enabled the synthesis of functionalized DKPs in high to excellent yields without any intermediate purification. The utility of this protocol has been demonstrated by synthesizing natural products, phomamide and Cyclo(Deala-l-Leu).
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Affiliation(s)
- Masayoshi Koshizuka
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Kaito Shinoda
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Kazuishi Makino
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Naoyuki Shimada
- Laboratory of Organic Chemistry for Molecular Transformations, Department of Chemistry and the Institute of Natural Sciences, Nihon University, Tokyo 156-8550, Japan
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42
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Al-Khdhairawi AAQ, Loo JSE, Abd Mutalib N, Abd Latip N, Manshoor N, Abu Bakar H, Babu Shivanagere Nagojappa N, Weber JF. Diketopiperazine and isoindolinone alkaloids from the endophytic fungus Aspergillus sp. HAB10R12. PHYTOCHEMISTRY 2023; 211:113685. [PMID: 37088350 DOI: 10.1016/j.phytochem.2023.113685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/31/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Four previously undescribed alkaloids, aspergillinine A-D, and four known diterpene pyrones were isolated from the potato dextrose agar (PDA) culture of Aspergillus sp. HAB10R12. The chemical structures of the isolated compounds were elucidated based on a detailed analysis of their NMR and MS data. The absolute configuration of the isolated compounds was determined by Electronic Circular Dichroism analysis coupled with computational methods. Aspergillinine A represents the first example of a diketopiperazine dipeptide containing the unnatural amino acid N-methyl kynurenine. Its absolute configuration revealed that it adopts a rather unusual conformation. Aspergillinine B represents a previously unencountered skeleton containing an isoindolinone ring. Aspergillinine C and D were similar to previously isolated diketopiperazine alkaloids, namely, lumpidin and brevianamide F, respectively. The diterpene pyrones were isolated twice previously, once from a soil-derived Aspergillus species, and once from the liquid culture of Aspergillus sp. HAB10R12. The alkaloids isolated in this study showed no antiproliferative activity when tested against HepG2 and A549 cancer cell lines.
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Affiliation(s)
- Amjad Ayad Qatran Al-Khdhairawi
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University Lakeside Campus, 47500, Subang Jaya, Selangor, Malaysia; Organic Synthesis Group, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281-S4, Ghent, 9000, Belgium.
| | - Jason Siau Ee Loo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University Lakeside Campus, 47500, Subang Jaya, Selangor, Malaysia; Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health & Medical Sciences, Taylor's University, No. 1, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia
| | - Nurliana Abd Mutalib
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA (UiTM), 42300, Selangor, Malaysia
| | - Normala Abd Latip
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA (UiTM), 42300, Selangor, Malaysia
| | - Nurhuda Manshoor
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA (UiTM), 42300, Selangor, Malaysia
| | - Hamidah Abu Bakar
- PICOMS International University College, 68100, Kuala Lumpur, Malaysia; Faculty of Health Sciences, Universiti Selangor, 40000, Selangor, Malaysia
| | | | - Jean-Frédéric Weber
- UFR Sciences Pharmaceutiques and INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC, 1366, ISVV, Univ. Bordeaux, 210 Chemin de Leysotte, Villenave d'Ornon, 33882, France
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Rakipov I, Akhmadiyarov A, Petrov A, Khachatrian A, Solomonov B. The Solvation Effect of C=O Group of Cyclic Anhydrides in Solution. Int J Mol Sci 2023; 24:ijms24076724. [PMID: 37047697 PMCID: PMC10095546 DOI: 10.3390/ijms24076724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/16/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
The paper reports the results of investigation intermolecular interactions between alanine and sarcosine anhydride in organic solvents. The absorption frequencies of cyclic dipeptide in solvents were measured by IR spectroscopy. The effect of Van der Waals interactions and the hydrogen bonding of solvents on absorption frequencies of the C=O group of anhydrides was discussed. The spectroscopic parameters for C=O∙∙∙H-O hydrogen bonding complexes of anhydride with methanol in aprotic and proton donor solvent are obtained. In multi-particle complexes of dipeptides with aliphatic alcohols, the hydrogen bond enhancement was between 10 and 16%, which is significantly lower than it is for amide complexes.
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Affiliation(s)
- Ilnaz Rakipov
- Department of Physical Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Aydar Akhmadiyarov
- Department of Physical Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Artem Petrov
- Department of Physical Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Artashes Khachatrian
- Department of Physical Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Boris Solomonov
- Department of Physical Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
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Xu ZZ, Zhuang Z, Cai R, Lin GQ, She Z, Zhao Q, He QL. Hydroxylation with Unusual Stereoinversion Catalyzed by an Fe II /2-OG Dependent Oxidase and 3,6-Diene-2,5-diketopiperazine Formation in the Biosynthesis of Brevianamide K. Angew Chem Int Ed Engl 2023; 62:e202216989. [PMID: 36750406 DOI: 10.1002/anie.202216989] [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: 11/21/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/09/2023]
Abstract
Natural products with the 3,6-diene-2,5-diketopiperazine core are widely distributed in nature; however, the biosynthetic mechanism of 3,6-diene-2,5-diketopiperazine in fungi remains to be further elucidated. Through heterologous expression and biochemical investigation of an FeII /2-oxoglutarate-dependent oxidase (AspE) and a heme-dependent P450 enzyme (AspF), we report that AspE, AspF and subsequent dehydration account for the formation of the 3,6-diene-2,5-diketopiperazine substructure of brevianamide K from Aspergillus sp. SK-28, a symbiotic fungus of mangrove plant Kandelia candel. More interestingly, in-depth investigation of the enzymatic mechanism showed that AspE promotes hydroxylation of brevianamide Q with unprecedented stereoinversion through hydrogen atom abstraction and water nucleophilic attack from the opposite face of the resultant iminium cation intermediate.
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Affiliation(s)
- Zhuo-Zheng Xu
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Zheng Zhuang
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Runlin Cai
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Guo-Qiang Lin
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Zhigang She
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qunfei Zhao
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Qing-Li He
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
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Amr K, Ibrahim N, Elissawy AM, Singab ANB. Unearthing the fungal endophyte Aspergillus terreus for chemodiversity and medicinal prospects: a comprehensive review. Fungal Biol Biotechnol 2023; 10:6. [PMID: 36966331 PMCID: PMC10040139 DOI: 10.1186/s40694-023-00153-2] [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: 01/18/2023] [Accepted: 02/22/2023] [Indexed: 03/27/2023] Open
Abstract
Aspergillus terreus microorganism represents a promising prospective source for drug discovery since it is rich in diverse kinds of bioactive secondary metabolites. It contributed to many biotechnological applications and its metabolites are used in the synthesis of certain pharmaceuticals and food products, in addition to its useful uses in fermentation processes. There are about 346 compounds identified from marine and terrestrial-derived A. terreus from 1987 until 2022, 172 compounds of them proved a vast array of bioactivity. This review aimed to create an up-to-date comprehensive literature data of A. terreus's secondary metabolites classes supported by its different bioactivity data to be a scientific record for the next work in drug discovery.
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Affiliation(s)
- Khadiga Amr
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, Cairo, 11566, Egypt
| | - Nehal Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, Cairo, 11566, Egypt
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, Cairo, 11566, Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University, Organization of African Unity Street 1, Cairo, 11566, Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Organization of African Unity Street 1, Cairo, 11566, Egypt.
- Center of Drug Discovery Research and Development, Ain-Shams University, Organization of African Unity Street 1, Cairo, 11566, Egypt.
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46
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Pinčeková L, Jančiová E, Berkeš D, Gyepes R, Kolarovič A, Caletková O. Total Synthesis of Hemerocallisamine I Paved by Gram-Scale Synthesis of (2 S,4 S)-4-Hydroxyglutamic Acid Lactone. Molecules 2023; 28:molecules28052177. [PMID: 36903423 PMCID: PMC10037412 DOI: 10.3390/molecules28052177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
Total synthesis of the 2-formylpyrrole alkaloid hemerocallisamine I is presented, both in racemic and enantiopure form. Our synthetic strategy involves (2S,4S)-4-hydroxyglutamic acid lactone as the key intermediate. Starting from an achiral substrate, the target stereogenic centers were introduced by means of crystallization-induced diastereomer transformation (CIDT) in a highly stereoselective fashion. A Maillard-type condensation was crucial to constructing the desired pyrrolic scaffold.
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Affiliation(s)
- Lucia Pinčeková
- Institute of Organic Chemistry, Catalysis and Petrochemistry, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Eva Jančiová
- Institute of Organic Chemistry, Catalysis and Petrochemistry, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Dušan Berkeš
- Institute of Organic Chemistry, Catalysis and Petrochemistry, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Róbert Gyepes
- Department of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 40 Prague, Czech Republic
| | - Andrej Kolarovič
- Department of Chemistry, Faculty of Education, Trnava University, Priemyselná 4, 918 43 Trnava, Slovakia
| | - Oľga Caletková
- Institute of Organic Chemistry, Catalysis and Petrochemistry, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
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Deigin V, Premyslova M, Ksenofontova O, Yatskin O, Volpina O. Evaluation of Neuroprotective and Adjuvant Activities of Diketopiperazine‐Based Peptidomimetics. ChemistrySelect 2023. [DOI: 10.1002/slct.202204076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Vladislav Deigin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho- Maklaya St., 16/10 Moscow 117997 Russia
- Immunotech Developments Inc. 2395 Speakman Drive, Suite 2025 Mississauga Ontario L5 K 1B3 Canada
| | - Marina Premyslova
- Immunotech Developments Inc. 2395 Speakman Drive, Suite 2025 Mississauga Ontario L5 K 1B3 Canada
| | - Olga Ksenofontova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho- Maklaya St., 16/10 Moscow 117997 Russia
| | - Oleg Yatskin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho- Maklaya St., 16/10 Moscow 117997 Russia
| | - Olga Volpina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho- Maklaya St., 16/10 Moscow 117997 Russia
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48
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Wang R, Piggott AM, Chooi YH, Li H. Discovery, bioactivity and biosynthesis of fungal piperazines. Nat Prod Rep 2023; 40:387-411. [PMID: 36374102 DOI: 10.1039/d2np00070a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Covering: up to the end of July, 2022Fungi are prolific producers of piperazine alkaloids, which have been shown to exhibit an array of remarkable biological activities. Since the first fungal piperazine, herquline A, was reported from Penicillium herquei Fg-372 in 1979, a plethora of structurally diverse piperazines have been isolated and characterised from various fungal strains. Significant advancements have been made in recent years towards unravelling the biosynthesis of fungal piperazines and numerous synthetic routes have been proposed. This review provides a comprehensive summary of the current knowledge of the discovery, classification, bioactivity and biosynthesis of piperazine alkaloids reported from fungi, and discusses the perspectives for exploring the structural diversity of fungal piperazines via genome mining of the untapped piperazine biosynthetic pathways.
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Affiliation(s)
- Rui Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, People's Republic of China.
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Hang Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, People's Republic of China.
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49
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Gödtel P, Starrett J, Pianowski ZL. Heterocyclic Hemipiperazines: Water-Compatible Peptide-Derived Photoswitches. Chemistry 2023; 29:e202204009. [PMID: 36790823 DOI: 10.1002/chem.202204009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/16/2023]
Abstract
Hemipiperazines are a recently discovered class of peptide-derived molecular photoswitches with high biocompatibility and therapeutic potential. Here, for the first time we describe photochromism of heterocyclic hemipiperazines. They demonstrate long thermal lifetimes, and enlarged band separation between photoisomers. Efficient photoisomerization occurs under aqueous conditions, although with a need for organic co-solvent. Bidirectional switching with visible light is observed for an extended aromatic system.
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Affiliation(s)
- Peter Gödtel
- Institute of Organic Chemistry, Karlsruhe Institute of Technology KIT, 76131, Karlsruhe, Germany
| | - Jessica Starrett
- Institute of Organic Chemistry, Karlsruhe Institute of Technology KIT, 76131, Karlsruhe, Germany
| | - Zbigniew L Pianowski
- Institute of Organic Chemistry, Karlsruhe Institute of Technology KIT, 76131, Karlsruhe, Germany
- Institute of Biological and Chemical Systems - FMS, Karlsruhe Institute of Technology KIT, 76344, Eggenstein-Leopoldshafen, Germany
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50
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Liu J, Li SM. Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria. Chembiochem 2023; 24:e202200502. [PMID: 36098493 PMCID: PMC10092475 DOI: 10.1002/cbic.202200502] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/12/2022] [Indexed: 02/04/2023]
Abstract
Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.,Current address: Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
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