1
|
Fischle A, Lutsch M, Hübner F, Schäker-Hübner L, Schürmann L, Hansen FK, Kalinina SA. Micro-scale screening of genetically modified Fusarium fujikuroi strain extends the apicidin family. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:51. [PMID: 39177677 DOI: 10.1007/s13659-024-00473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024]
Abstract
Apicidins are a class of naturally occurring cyclic tetrapeptides produced by few strains within the Fusarium genus. These secondary metabolites have gained significant attention due to their antiprotozoal activity through HDAC inhibition, thereby highlighting their potential for the treatment of malaria. Predominantly, apicidins have been isolated from Fusarium semitectum, offering a deep insight into the biosynthetic pathway responsible for their formation. A similar biosynthetic gene cluster has also been identified in the rice pathogenic fungus F. fujikuroi, leading the discovery of three additional apicidins through genetic manipulation. Routine mass spectrometric screening of these compound-producing strains revealed another metabolite structurally related to previously studied apicidins. By optimizing culture conditions and developing an effective isolation method, we obtained a highly pure substance, whose chemical structure was fully elucidated using NMR and HRMS fragmentation. Further studies were conducted to determine cytotoxicity, antimalarial activity, and HDAC inhibitory activity of this new secondary metabolite alongside the previously known apicidins. This work not only expands the apicidin class with a new member but also provides extensive insights and comparative analysis of apicidin-like substances produced by F. fujikuroi.
Collapse
Affiliation(s)
- Alica Fischle
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
- Graduate School of Natural Products, Corrensstraße 43, 48149, Münster, Germany
| | - Mika Lutsch
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Florian Hübner
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Linda Schäker-Hübner
- Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An Der Immenburg 4, 53121, Bonn, Germany
| | - Lina Schürmann
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An Der Immenburg 4, 53121, Bonn, Germany
| | - Svetlana A Kalinina
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany.
- Graduate School of Natural Products, Corrensstraße 43, 48149, Münster, Germany.
| |
Collapse
|
2
|
Liu XY, Huang JC, Zhang T, Wang HR, Xu QH, Xia YG, Xu AJ, Yang ZY, Sun L, Zhao WJ, Zhao J, Qian F, Hou AJ. Cyclo(L-Pro-L-Trp) from Chilobrachys jingzhao alleviates formalin-induced inflammatory pain by suppressing the inflammatory response and inhibiting TRAF6-mediated MAPK and NF-κB signaling pathways. Int Immunopharmacol 2024; 139:112602. [PMID: 39033660 DOI: 10.1016/j.intimp.2024.112602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024]
Abstract
Chronic pain has emerged as a significant public health issue, seriously affecting patients' quality of life and psychological well-being, with a lack of effective pharmacological treatments. Numerous studies have indicated that macrophages play a crucial role in inflammatory pain, and targeting neuro-immune interactions for drug development may represent a promising direction for pain management. Chilobrachys jingzhao (C. jingzhao) is used as a folk medicine of the Li nationality with the efficacy of eliminating swelling, detoxicating, and relieving pain, and the related products are widely used in the market. However, the chemical constituents of C. jingzhao have not been reported, and the pharmacodynamic substance and the precise functional mechanism are unrevealed. Here we isolated a cyclic dipeptide, cyclo(L-Pro-L-Trp) (CPT) from C. jingzhao for the first time. CPT remarkably alleviated formalin-induced inflammatory pain and significantly inhibited inflammatory responses. In vivo, CPT attenuated neutrophil infiltration and plantar tissue edema and suppressed the mRNA expression of pro-inflammatory molecules. In vitro, CPT suppressed inflammation triggered by lipopolysaccharide (LPS) in both RAW 264.7 and iBMDM cells, reducing expressions of inducible nitric oxide synthase (iNOS), superoxide, and pro-inflammatory molecules. A mechanistic study revealed that CPT exerted an anti-inflammatory activity by blocking the mitogen-activated protein kinases (MAPK) and nuclear factor-kappa B (NF-κB) signaling pathways, as well as alleviating the ubiquitination of tumor necrosis factor receptor-associated factor 6 (TRAF6). Our results elucidated the pharmacodynamic material basis of C. jingzhao, and CPT can be a promising lead for alleviating inflammation and inflammatory pain.
Collapse
Affiliation(s)
- Xin-Yue Liu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin-Chang Huang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Zhang
- Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, 358 Datong Road, Pudong New District, Shanghai 200137, China
| | - Han-Rui Wang
- Hainan Spider King Biotechnology Co., Ltd., Haikou 570125, China
| | - Qi-Hui Xu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Gui Xia
- Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing 210008, China
| | - A-Jing Xu
- Department of Clinical Pharmacy, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Ze-Yong Yang
- Department of Anesthesiology, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Lei Sun
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wen-Juan Zhao
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Zhao
- Hainan Spider King Biotechnology Co., Ltd., Haikou 570125, China.
| | - Feng Qian
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ai-Jun Hou
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
3
|
Chen H, Zhang Y, Wen Y, Fan X, Sciolino N, Lin Y, Breindel L, Dai Y, Shekhtman A, Xue XS, Zhang Q. Production of constrained L-cyclo-tetrapeptides by epimerization-resistant direct aminolysis. Nat Commun 2024; 15:5372. [PMID: 38918367 PMCID: PMC11199569 DOI: 10.1038/s41467-024-49329-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/30/2024] [Indexed: 06/27/2024] Open
Abstract
The synthesis of constrained 12-membered rings is notably difficult. The main challenges result from constraints during the linear peptide cyclization. Attempts to overcome constraints through excessive activation frequently cause peptidyl epimerization, while insufficient activation of the C-terminus hampers cyclization and promotes intermolecular oligomer formation. We present a β-thiolactone framework that enables the synthesis of cyclo-tetrapeptides via direct aminolysis. This tactic utilizes a mechanism that restricts C-terminal carbonyl rotation while maintaining high reactivity, thereby enabling efficient head-to-tail amidation, reducing oligomerization, and preventing epimerization. A broad range of challenging cyclo-tetrapeptides ( > 20 examples) are synthesized in buffer and exhibits excellent tolerance toward nearly all proteinogenic amino acids. Previously unattainable macrocycles, such as cyclo-L-(Pro-Tyr-Pro-Val), have been produced and identified as μ-opioid receptor (MOR) agonists, with an EC50 value of 2.5 nM. Non-epimerizable direct aminolysis offers a practical solution for constrained peptide cyclization, and the discovery of MOR agonist activity highlights the importance of overcoming synthetic challenges for therapeutic development.
Collapse
Affiliation(s)
- Huan Chen
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA
| | - Yuchen Zhang
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China
| | - Yuming Wen
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA
| | - Xinhao Fan
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA
| | - Nicholas Sciolino
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA
| | - Yanyun Lin
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA
| | - Leonard Breindel
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA
| | - Yuanwei Dai
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA.
| | - Xiao-Song Xue
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, 200032, Shanghai, China.
| | - Qiang Zhang
- Department of Chemistry, State University of New York, University at Albany, Albany, NY, 12222, USA.
| |
Collapse
|
4
|
Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
Collapse
Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
| |
Collapse
|
5
|
Yamada A, Takei T, Kawakami T, Taniguchi Y, Sekiguchi K, Hojo H. Application of cysteinyl prolyl ester for the synthesis of cyclic peptides containing an RGD sequence and their biological activity measurement. Front Chem 2024; 12:1391678. [PMID: 38873405 PMCID: PMC11169864 DOI: 10.3389/fchem.2024.1391678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024] Open
Abstract
Cysteinyl RGD-peptidyl cysteinyl prolyl esters, which have different configurations at the cysteine and proline residues, were synthesized by the solid-phase method and cyclized by the native chemical ligation reaction. Cyclization efficiently proceeded to give cyclic peptides, regardless of the difference in the configuration. The peptides were further derivatized to the corresponding desulfurized or methylated cyclic peptides at the Cys residues. The inhibition activity to αvβ6 integrin binding was then analyzed by ELISA. The results showed that the activity varied depending on the difference in the configuration and modification of the cysteinyl prolyl ester (CPC) moiety, demonstrating the usefulness of this method in the search for a good inhibitor of the protein-protein interaction.
Collapse
Affiliation(s)
| | | | | | | | | | - Hironobu Hojo
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
6
|
Saunders GJ, Spring SA, Jayawant E, Wilkening I, Roesner S, Clarkson GJ, Dixon AM, Notman R, Shipman M. Synthesis and Functionalization of Azetidine-Containing Small Macrocyclic Peptides. Chemistry 2024; 30:e202400308. [PMID: 38488326 DOI: 10.1002/chem.202400308] [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: 02/25/2024] [Indexed: 04/11/2024]
Abstract
Cyclic peptides are increasingly important structures in drugs but their development can be impeded by difficulties associated with their synthesis. Here, we introduce the 3-aminoazetidine (3-AAz) subunit as a new turn-inducing element for the efficient synthesis of small head-to-tail cyclic peptides. Greatly improved cyclizations of tetra-, penta- and hexapeptides (28 examples) under standard reaction conditions are achieved by introduction of this element within the linear peptide precursor. Post-cyclization deprotection of the amino acid side chains with strong acid is realized without degradation of the strained four-membered azetidine. A special feature of this chemistry is that further late-stage modification of the resultant macrocyclic peptides can be achieved via the 3-AAz unit. This is done by: (i) chemoselective deprotection and substitution at the azetidine nitrogen, or by (ii) a click-based approach employing a 2-propynyl carbamate on the azetidine nitrogen. In this way, a range of dye and biotin tagged macrocycles are readily produced. Structural insights gained by XRD analysis of a cyclic tetrapeptide indicate that the azetidine ring encourages access to the less stable, all-trans conformation. Moreover, introduction of a 3-AAz into a representative cyclohexapeptide improves stability towards proteases compared to the homodetic macrocycle.
Collapse
Affiliation(s)
- George J Saunders
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Sam A Spring
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Eleanor Jayawant
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Stefan Roesner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Guy J Clarkson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Michael Shipman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
- The Palatine Centre, Stockton Road, Durham, DH1 3LE, U.K
| |
Collapse
|
7
|
Salveson PJ, Moyer AP, Said MY, Gӧkçe G, Li X, Kang A, Nguyen H, Bera AK, Levine PM, Bhardwaj G, Baker D. Expansive discovery of chemically diverse structured macrocyclic oligoamides. Science 2024; 384:420-428. [PMID: 38662830 DOI: 10.1126/science.adk1687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Small macrocycles with four or fewer amino acids are among the most potent natural products known, but there is currently no way to systematically generate such compounds. We describe a computational method for identifying ordered macrocycles composed of alpha, beta, gamma, and 17 other amino acid backbone chemistries, which we used to predict 14.9 million closed cycles composed of >42,000 monomer combinations. We chemically synthesized 18 macrocycles predicted to adopt single low-energy states and determined their x-ray or nuclear magnetic resonance structures; 15 of these were very close to the design models. We illustrate the therapeutic potential of these macrocycle designs by developing selective inhibitors of three protein targets of current interest. By opening up a vast space of readily synthesizable drug-like macrocycles, our results should considerably enhance structure-based drug design.
Collapse
Affiliation(s)
- Patrick J Salveson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Meerit Y Said
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Gizem Gӧkçe
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Xinting Li
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Hannah Nguyen
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Paul M Levine
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
8
|
Thakur DG, Rathod NB, Patel SD, Patel DM, Patel RN, Sonawane MA, Ghosh SC. Palladium-Catalyzed Chelation-Assisted Aldehyde C-H Bond Activation of Quinoline-8-carbaldehydes: Synthesis of Amides from Aldehydes with Anilines and Other Amines. J Org Chem 2024. [PMID: 38195393 DOI: 10.1021/acs.joc.3c02139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
A palladium-catalyzed chelation-assisted direct aldehyde C-H bond amidation of quinoline-8-carbaldehydes with an amine was developed under mild reaction conditions. A wide range of amides were obtained in good to excellent yields from aldehyde with a variety of aniline derivatives and aliphatic amines. Our methodology was successfully applied to synthesize known DNA intercalating agents and can be easily scaled up to a gram scale.
Collapse
Affiliation(s)
- Dinesh Gopichand Thakur
- Natural Products and Green Chemistry Division, Central Salt and Marine Chemicals Research Institute (CSIR), G. B. Marg, Bhavnagar , Gujarat 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nileshkumar B Rathod
- Natural Products and Green Chemistry Division, Central Salt and Marine Chemicals Research Institute (CSIR), G. B. Marg, Bhavnagar , Gujarat 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sachinkumar D Patel
- Natural Products and Green Chemistry Division, Central Salt and Marine Chemicals Research Institute (CSIR), G. B. Marg, Bhavnagar , Gujarat 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Dharmik M Patel
- Natural Products and Green Chemistry Division, Central Salt and Marine Chemicals Research Institute (CSIR), G. B. Marg, Bhavnagar , Gujarat 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Raj N Patel
- Natural Products and Green Chemistry Division, Central Salt and Marine Chemicals Research Institute (CSIR), G. B. Marg, Bhavnagar , Gujarat 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mahesh A Sonawane
- Natural Products and Green Chemistry Division, Central Salt and Marine Chemicals Research Institute (CSIR), G. B. Marg, Bhavnagar , Gujarat 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Subhash Chandra Ghosh
- Natural Products and Green Chemistry Division, Central Salt and Marine Chemicals Research Institute (CSIR), G. B. Marg, Bhavnagar , Gujarat 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
9
|
Budimir ZL, Patel RS, Eggly A, Evans CN, Rondon-Cordero HM, Adams JJ, Das C, Parkinson EI. Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase. Nat Chem Biol 2024; 20:120-128. [PMID: 38062262 PMCID: PMC10999230 DOI: 10.1038/s41589-023-01495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for chemical tools and potential therapeutics. Synthetic methods for peptide macrocyclization are often hampered by C-terminal epimerization and oligomerization, leading to difficult scalability. While chemical strategies to circumvent this issue exist, they often require specific amino acids to be present in the peptide sequence. Herein, we report the characterization of Ulm16, a peptide cyclase belonging to the penicillin-binding protein-type class of thioesterases that catalyze head-to-tail macrolactamization of nonribosmal peptides. Ulm16 efficiently cyclizes various nonnative peptides ranging from 4 to 6 amino acids with catalytic efficiencies of up to 3 × 106 M-1 s-1. Unlike many previously described homologs, Ulm16 tolerates a variety of C- and N-terminal amino acids. The crystal structure of Ulm16, along with modeling of its substrates and site-directed mutagenesis, allows for rationalization of this wide substrate scope. Overall, Ulm16 represents a promising tool for the biocatalytic production of macrocyclic peptides.
Collapse
Affiliation(s)
| | - Rishi S Patel
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Alyssa Eggly
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Claudia N Evans
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Jessica J Adams
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
10
|
Su L, Deng H. Size matters. Nat Chem Biol 2024; 20:8-10. [PMID: 38114808 DOI: 10.1038/s41589-023-01503-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Affiliation(s)
- Li Su
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen, UK.
| |
Collapse
|
11
|
Ho TT, Peng C, Seto E, Lin H. Trapoxin A Analogue as a Selective Nanomolar Inhibitor of HDAC11. ACS Chem Biol 2023; 18:803-809. [PMID: 36977486 PMCID: PMC10127203 DOI: 10.1021/acschembio.2c00840] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Histone deacetylases (HDACs) are enzymes that regulate many important biological pathways. There is a need for the development of isoform-selective HDAC inhibitors for further biological applications. Here, we report the development of trapoxin A analogues as potent and selective inhibitors of HDAC11, an enzyme that can efficiently remove long-chain fatty acyl groups from proteins. In particular, we show that one of the trapoxin A analogues, TD034, has nanomolar potency in enzymatic assays. We show that in cells, TD034 is active at low micromolar concentrations and inhibits the defatty acylation of SHMT2, a known HDAC11 substrate. The high potency and selectivity of TD034 would permit further development of HDAC11 inhibitors for biological and therapeutic applications.
Collapse
Affiliation(s)
- Thanh Tu Ho
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Changmin Peng
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, George Washington Cancer Center, George Washington University, Washington, District of Columbia 20037, United States
| | - Edward Seto
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, George Washington Cancer Center, George Washington University, Washington, District of Columbia 20037, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
12
|
Ghosh U, Kumar V, Singh G, Kanti Chakraborty T. Conformation Based in silico Studies of Cyclic Tetrapeptides with βγ Fused Turns as Thrombin Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Uttam Ghosh
- Department of Organic Chemistry Indian Institute of Science Bengaluru 560012 India
| | - Vikash Kumar
- CSIR-Central Drug Research Institute Lucknow 226031 India
| | - Gajendra Singh
- CSIR-Central Drug Research Institute Lucknow 226031 India
- School of Life Sciences Central University of Rajasthan Bandar Sindri Ajmer 305817 Rajasthan India
| | | |
Collapse
|
13
|
Fumo VM, Roberts RC, Zhang J, O'Reilly MC. Diastereoselective synthesis of cyclic tetrapeptide pseudoxylallemycin A illuminates the impact of base during macrolactamization. Org Biomol Chem 2023; 21:1056-1069. [PMID: 36628602 PMCID: PMC11311250 DOI: 10.1039/d2ob02126a] [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: 01/07/2023]
Abstract
Therapeutic agents with unique molecular structures and new mechanisms of action are needed to confront the phenomenon of multidrug resistance among bacteria. Pseudoxylallemycins, cyclic tetrapeptide (CTP) natural products, have exhibited modest antibiotic activity, but their synthesis has proven challenging. Inherent ring strain in CTPs decreases the rate of cyclization in lieu of polymerization and racemization pathways, which has resulted in previous syntheses describing mixtures of diastereomers containing predominantly an undesired epimer. We have optimized the cyclization step of pseudoxylallemycin A to favor production of the natural diastereomer; notably, variation of the base, temperature, and solvent with peptide coupling reagent propylphosphonic anhydride (T3P) afforded exquisite selectivity for the natural product in as high as 97 : 3 DR, and our conditions can provide the natural product in up to 32% overall yield through 8 steps. Employing weaker bases than those typically used in peptide coupling reactions led to the greatest improvement in diastereoselectivity, and these studies demonstrated that the identity of the amine base has enormous impact on the rate of C-terminal epimerization when T3P is used, a variable usually considered of lesser consequence when combined with typical amide coupling reagents. Toward fully characterizing pseudoxylallemycin stereoisomers, variable temperature NMR was described as a tool to more clearly analyze CTPs that exhibit multiple conformational states. These synthetic and spectroscopic insights were applied toward synthesizing several natural product analogues, and their antibacterial activity was examined using microdilution assays.
Collapse
Affiliation(s)
- Vincent M Fumo
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
| | - R Charlie Roberts
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
| | - Jieyu Zhang
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
| | - Matthew C O'Reilly
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
| |
Collapse
|
14
|
Wills R, Adebomi V, Spancake C, Cohen RD, Raj M. Synthesis of L-cyclic tetrapeptides by backbone amide activation CyClick strategy. Tetrahedron 2022; 126:133071. [PMID: 37994371 PMCID: PMC10664817 DOI: 10.1016/j.tet.2022.133071] [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] [Indexed: 10/31/2022]
Abstract
Cyclic tetrapeptides exhibit high cellular permeability and a wide range of biological properties and thus have gained great interest in the field of medicinal chemistry. We synthesized highly strained 12-membered head to tail cyclic peptides with varying reactive amino acids, without oligomerization using the exclusively intramolecular CyClick chemistry. This occurs by a two-step process involving the low-energy formation of a 15 atom-containing cyclic imine, followed by a chemoselective ring contraction of the peptide backbone generating a highly strained 12 atom-containing cyclic tetrapeptide. This reaction exhibited high substrate scope and generated head to tail cyclic tetrapeptides with varying amino acids at the N-terminus, showing chemoselectivity without the need for side group protection.
Collapse
Affiliation(s)
- Rachel Wills
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | | | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
15
|
Synthesis of Cyclotetrapeptides Analogues to Natural Products as Herbicides. Molecules 2022; 27:molecules27217350. [PMID: 36364176 PMCID: PMC9656801 DOI: 10.3390/molecules27217350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
The synthesis of cyclotetrapeptides analogues of the natural products tentoxin and versicotide D was achieved in good yield by solid phase peptide synthesis (SPPS) of their linear precursors and solution phase cyclization. All the cyclopeptides and several open precursors were evaluated as herbicides. Five cyclopeptides and five lineal peptides showed a significant inhibition (>70%) of Ryegrass seed’s radicle growth at 67 μg/mL. The evaluation at lower concentrations (4−11 μM) indicates two cyclopeptides analogs of tentoxin, which present one (N-Methyl-d-Phe), and two N-MeAA (N-Methyl-Ala and N-Methyl-Phe), respectively, as the most active of them, showing remarkable phytotoxic activity. In two cases, the open precursors are as active as their corresponding cyclopeptide. However, many linear peptides are inactive and their cyclization derivatives showed herbicidal activity. In addition, two cyclopeptide analogues of versicotide D showed more improved activity than the natural product. The results indicate that the peptide sequence, the amino acid stereochemistry and the presence of N-methyl group have important influence on the phytotoxic activity. Moreover, several compounds could be considered as lead candidates in the development of bioherbicides.
Collapse
|
16
|
Muchlis HN, Kurnia DY, Maharani R, Zainuddin A, Harneti D, Nurlelasari, Mayanti T, Farabi K, Hidayat AT, Supratman U. Total Synthesis and Antimicrobial Evaluation of Xylapeptide A. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Handi Nugraha Muchlis
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Dessy Yulyani Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Rani Maharani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Laboratorium Sentral Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Achmad Zainuddin
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Desi Harneti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Nurlelasari
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Tri Mayanti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Kindi Farabi
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Laboratorium Sentral Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Ace Tatang Hidayat
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Laboratorium Sentral Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| | - Unang Supratman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Laboratorium Sentral Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
- Study Center of Natural products and Synthesis, Faculty of Mathematics and Natural Sciences Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang West Java Indonesia
| |
Collapse
|
17
|
On-resin peptide modification of methionine residue by employing 2-bromoacetate derivatives. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Han J, Wang H, Zhang R, Dai H, Chen B, Wang T, Sun J, Wang W, Song F, Li E, Lyu Z, Liu H. Cyclic Tetrapeptides with Synergistic Antifungal Activity from the Fungus Aspergillus westerdijkiae Using LC-MS/MS-Based Molecular Networking. Antibiotics (Basel) 2022; 11:166. [PMID: 35203768 PMCID: PMC8868193 DOI: 10.3390/antibiotics11020166] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 12/03/2022] Open
Abstract
Fungal natural products play a prominent role in the development of pharmaceuticalagents. Two new cyclic tetrapeptides (CTPs), westertide A (1) and B (2), with eight known compounds (3-10) were isolated from the fungus Aspergillus westerdijkiae guided by OSMAC (one strain-many compounds) and molecular networking strategies. The structures of new compounds were unambiguously determined by a combination of NMR and mass data analysis, and chemical methods. All of the isolates were evaluated for antimicrobial effects, synergistic antifungal activity, cytotoxic activity, and HDAC inhibitory activity. Compounds 1-2 showed synergistic antifungal activity against Candida albicans SC5314 with the presence of rapamycin and weak HDAC (histone deacetylase) inhibitory activity. These results indicate that molecular networking is an efficient approach for dereplication and identification of new CTPs. CTPs might be a good starting point for the development of synergistic antifungal agents.
Collapse
Affiliation(s)
- Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
| | - Hanying Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Rui Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
| | - Huanqin Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baosong Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
| | - Tao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
| | - Wenzhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
| | - Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China;
| | - Erwei Li
- Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhitang Lyu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (J.H.); (H.W.); (R.Z.); (H.D.); (B.C.); (T.W.); (J.S.); (W.W.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
19
|
Hartendorp APT, de Zwart FJ, Bieräugel H, Bruin BD, Reek JNH, van Maarseveen JH. Peptide cyclisation promoted by supramolecular complex formation. Org Biomol Chem 2022; 20:575-578. [PMID: 34935833 PMCID: PMC8767553 DOI: 10.1039/d1ob02309h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/16/2021] [Indexed: 12/02/2022]
Abstract
Phenol ester activated dipeptides that are reluctant to ring-close have been cyclised with the aid of sterically shielding metallo-porphyrins avoiding unwanted intermolecular reactions. The binding of ZnTPP to the dipyridine-functionalised activating phenolic ester was studied by NMR titrations and modelling. Staudinger-mediated cyclisations in the presence of ZnTPP increased the yield of the cyclic dipeptide from 16% to 40%.
Collapse
Affiliation(s)
- Arnout P T Hartendorp
- Van't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Felix J de Zwart
- Van't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Hans Bieräugel
- Van't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Bas de Bruin
- Van't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Joost N H Reek
- Van't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Jan H van Maarseveen
- Van't Hoff Institute for Molecular Sciences (HIMS), Science Park 904, 1098 XH Amsterdam, The Netherlands.
| |
Collapse
|
20
|
Li H, Li J, Chao J, Zhang Z, Qin C. Head-to-tail cyclization for the synthesis of naturally occurring cyclic peptides on organophosphorus small-molecular supports. Org Chem Front 2022. [DOI: 10.1039/d1qo01362a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
4,4′-bis(diphenylphosphinyloxyl) diphenyl ketoxime and 4-diphenyl phospholoxy benzyl alcohol were designed and prepared as supports for peptide synthesis. The total synthesis of cyclic peptides in a resin-free manner was successfully demonstrated.
Collapse
Affiliation(s)
- Haidi Li
- MIIT Key Laboratory of Special Functional & Intelligent Polymer materials, MOE Key Laboratory of Supernormal Material Physics & Chemistry, Shaanxi Key Laboratory of Polymer Science & Technology, Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Junyou Li
- MIIT Key Laboratory of Special Functional & Intelligent Polymer materials, MOE Key Laboratory of Supernormal Material Physics & Chemistry, Shaanxi Key Laboratory of Polymer Science & Technology, Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Jie Chao
- MIIT Key Laboratory of Special Functional & Intelligent Polymer materials, MOE Key Laboratory of Supernormal Material Physics & Chemistry, Shaanxi Key Laboratory of Polymer Science & Technology, Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Zixin Zhang
- MIIT Key Laboratory of Special Functional & Intelligent Polymer materials, MOE Key Laboratory of Supernormal Material Physics & Chemistry, Shaanxi Key Laboratory of Polymer Science & Technology, Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Chuanguang Qin
- MIIT Key Laboratory of Special Functional & Intelligent Polymer materials, MOE Key Laboratory of Supernormal Material Physics & Chemistry, Shaanxi Key Laboratory of Polymer Science & Technology, Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| |
Collapse
|
21
|
Ramlawi S, Aitken A, Abusharkh S, McMullin DR, Avis TJ. Arthropeptide A, an antifungal cyclic tetrapeptide from Arthrobacter psychrophenolicus isolated from disease suppressive compost. Nat Prod Res 2021; 36:5715-5723. [PMID: 34933636 DOI: 10.1080/14786419.2021.2018434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In an effort to describe bioactive antifungal compounds from antagonistic bacteria with potential for biocontrol of plant pathogens, a strain of Arthrobacter psychrophenolicus was collected from plant disease suppressive compost prepared from composted material of marine origin. Few natural products have been characterized from the non-filamentous Actinobacteria genus Arthrobacter. A new cyclic tetrapeptide, cyclo-(L-Pro-L-Leu-L-γHyp-L-Tyr); arthropeptide A (1), was isolated from the EtOAc soluble culture filtrate extract of A. psychrophenolicus M9-17 grown in MOLP broth. Its structure was confirmed by HRMS, interpretation of NMR data, and a modified Marfey's method. Arthropeptide A (1) displayed antifungal activity towards Alternaria alternata, the causal agent of disease in numerous host plant species, which had shown the previous susceptibility to A. psychrophenolicus. The newly identified compound may be responsible, in part, for the inhibitory activity of the bacterium against fungal plant pathogens.
Collapse
Affiliation(s)
- Serine Ramlawi
- Department of Chemistry, Carleton University, Ottawa, ON, Canada
| | - Alex Aitken
- Department of Chemistry, Carleton University, Ottawa, ON, Canada
| | - Sawsan Abusharkh
- Department of Chemistry, Carleton University, Ottawa, ON, Canada
| | - David R McMullin
- Department of Chemistry, Carleton University, Ottawa, ON, Canada.,Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| | - Tyler J Avis
- Department of Chemistry, Carleton University, Ottawa, ON, Canada.,Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| |
Collapse
|
22
|
Qiu X, Zhu L, Wang H, Tan Y, Yang Z, Yang L, Wan L. From natural products to HDAC inhibitors: An overview of drug discovery and design strategy. Bioorg Med Chem 2021; 52:116510. [PMID: 34826681 DOI: 10.1016/j.bmc.2021.116510] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/09/2021] [Accepted: 10/15/2021] [Indexed: 02/08/2023]
Abstract
Histone deacetylases (HDACs) play a key role in the homeostasis of protein acetylation in histones and have recently emerged as a therapeutic target for numerous diseases. The inhibition of HDACs may block angiogenesis, arrest cell growth, and lead to differentiation and apoptosis in tumour cells. Thus, HDAC inhibitors (HDACi) have received increasing attention and many of which are developed from natural sources. In the past few decades, naturally occurring HDACi have been identified to have potent anticancer activities, some of which have demonstrated promising therapeutic effects on haematological malignancies. In this review, we summarized the discovery and modification of HDAC inhibitors from natural sources, novel drug design that uses natural products as parent nuclei, and dual target design strategies that combine HDAC with non-HDAC targets.
Collapse
Affiliation(s)
- Xiang Qiu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lv Zhu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Huan Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan Tan
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhuang Yang
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Linyu Yang
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li Wan
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| |
Collapse
|
23
|
Dard C, Leforestier B, Francisco Hilário F, Traoré MDM, Lespinasse MA, Pérès B, Molina MC, Pereira de Freitas R, Milet A, Maubon D, Wong YS. Crossing of the Cystic Barriers of Toxoplasma gondii by the Fluorescent Coumarin Tetra-Cyclopeptide. Molecules 2021; 26:7506. [PMID: 34946588 PMCID: PMC8708940 DOI: 10.3390/molecules26247506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/28/2021] [Accepted: 12/05/2021] [Indexed: 01/11/2023] Open
Abstract
FR235222 is a natural tetra-cyclopeptide with a strong inhibition effect on histone deacetylases, effective on mammalian cells as well as on intracellular apicomplexan parasites, such as Toxoplasma gondii, in the tachyzoite and bradyzoite stages. This molecule is characterized by two parts: the zinc-binding group, responsible for the binding to the histone deacetylase, and the cyclic tetrapeptide moiety, which plays a crucial role in cell permeability. Recently, we have shown that the cyclic tetrapeptide coupled with a fluorescent diethyl-amino-coumarin was able to maintain properties of cellular penetration on human cells. Here, we show that this property can be extended to the crossing of the Toxoplasma gondii cystic cell wall and the cell membrane of the parasite in its bradyzoite form, while maintaining a high efficacy as a histone deacetylase inhibitor. The investigation by molecular modeling allows a better understanding of the penetration mechanism.
Collapse
Affiliation(s)
- Céline Dard
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM, CNRSINSERM U1209, CNRS UMR 5309, Univ. Grenoble Alpes, 38000 Grenoble, France; (C.D.); (D.M.)
| | - Baptiste Leforestier
- Team SITH, CNRS UMR 5250, Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France; (B.L.); (A.M.)
| | - Flaviane Francisco Hilário
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Mohamed Dit Mady Traoré
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Marie-Ange Lespinasse
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Basile Pérès
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Marie-Carmen Molina
- Team COMET, CNRS UMR 5063, Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France; (F.F.H.); (M.D.M.T.); (M.-A.L.); (B.P.); (M.-C.M.)
| | - Rossimiriam Pereira de Freitas
- Departamento de Química, Universidade Federal de Minas Gerais, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil;
| | - Anne Milet
- Team SITH, CNRS UMR 5250, Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France; (B.L.); (A.M.)
| | - Danièle Maubon
- Team Host-Pathogen Interactions and Immunity to Infection, Institute for Advanced Biosciences, INSERM, CNRSINSERM U1209, CNRS UMR 5309, Univ. Grenoble Alpes, 38000 Grenoble, France; (C.D.); (D.M.)
| | - Yung-Sing Wong
- Departamento de Química, Universidade Federal de Minas Gerais, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil;
| |
Collapse
|
24
|
Natural Peptides Inducing Cancer Cell Death: Mechanisms and Properties of Specific Candidates for Cancer Therapeutics. Molecules 2021; 26:molecules26247453. [PMID: 34946535 PMCID: PMC8708364 DOI: 10.3390/molecules26247453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 01/10/2023] Open
Abstract
Nowadays, cancer has become the second highest leading cause of death, and it is expected to continue to affect the population in forthcoming years. Additionally, treatment options will become less accessible to the public as cases continue to grow and disease mechanisms expand. Hence, specific candidates with confirmed anticancer effects are required to develop new drugs. Among the novel therapeutic options, proteins are considered a relevant source, given that they have bioactive peptides encrypted within their sequences. These bioactive peptides, which are molecules consisting of 2–50 amino acids, have specific activities when administered, producing anticancer effects. Current databases report the effects of peptides. However, uncertainty is found when their molecular mechanisms are investigated. Furthermore, analyses addressing their interaction networks or their directly implicated mechanisms are needed to elucidate their effects on cancer cells entirely. Therefore, relevant peptides considered as candidates for cancer therapeutics with specific sequences and known anticancer mechanisms were accurately reviewed. Likewise, those features which turn certain peptides into candidates and the mechanisms by which peptides mediate tumor cell death were highlighted. This information will make robust the knowledge of these candidate peptides with recognized mechanisms and enhance their non-toxic capacity in relation to healthy cells and further avoid cell resistance.
Collapse
|
25
|
Trinidad-Calderón PA, Varela-Chinchilla CD, García-Lara S. Natural Peptides Inducing Cancer Cell Death: Mechanisms and Properties of Specific Candidates for Cancer Therapeutics. Molecules 2021. [DOI: https://doi.org/10.3390/molecules26247453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nowadays, cancer has become the second highest leading cause of death, and it is expected to continue to affect the population in forthcoming years. Additionally, treatment options will become less accessible to the public as cases continue to grow and disease mechanisms expand. Hence, specific candidates with confirmed anticancer effects are required to develop new drugs. Among the novel therapeutic options, proteins are considered a relevant source, given that they have bioactive peptides encrypted within their sequences. These bioactive peptides, which are molecules consisting of 2–50 amino acids, have specific activities when administered, producing anticancer effects. Current databases report the effects of peptides. However, uncertainty is found when their molecular mechanisms are investigated. Furthermore, analyses addressing their interaction networks or their directly implicated mechanisms are needed to elucidate their effects on cancer cells entirely. Therefore, relevant peptides considered as candidates for cancer therapeutics with specific sequences and known anticancer mechanisms were accurately reviewed. Likewise, those features which turn certain peptides into candidates and the mechanisms by which peptides mediate tumor cell death were highlighted. This information will make robust the knowledge of these candidate peptides with recognized mechanisms and enhance their non-toxic capacity in relation to healthy cells and further avoid cell resistance.
Collapse
|
26
|
Herlan CN, Sonnefeld A, Gloge T, Brückel J, Schlee LC, Muhle-Goll C, Nieger M, Bräse S. Macrocyclic Tetramers-Structural Investigation of Peptide-Peptoid Hybrids. Molecules 2021; 26:molecules26154548. [PMID: 34361700 PMCID: PMC8348019 DOI: 10.3390/molecules26154548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 11/16/2022] Open
Abstract
Outstanding affinity and specificity are the main characteristics of peptides, rendering them interesting compounds for basic and medicinal research. However, their biological applicability is limited due to fast proteolytic degradation. The use of mimetic peptoids overcomes this disadvantage, though they lack stereochemical information at the α-carbon. Hybrids composed of amino acids and peptoid monomers combine the unique properties of both parent classes. Rigidification of the backbone increases the affinity towards various targets. However, only little is known about the spatial structure of such constrained hybrids. The determination of the three-dimensional structure is a key step for the identification of new targets as well as the rational design of bioactive compounds. Herein, we report the synthesis and the structural elucidation of novel tetrameric macrocycles. Measurements were taken in solid and solution states with the help of X-ray scattering and NMR spectroscopy. The investigations made will help to find diverse applications for this new, promising compound class.
Collapse
Affiliation(s)
- Claudine Nicole Herlan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Anna Sonnefeld
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Thomas Gloge
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Julian Brückel
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Luisa Chiara Schlee
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Martin Nieger
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland;
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Correspondence:
| |
Collapse
|
27
|
Muramatsu W, Hattori T, Yamamoto H. Amide bond formation: beyond the dilemma between activation and racemisation. Chem Commun (Camb) 2021; 57:6346-6359. [PMID: 34121110 DOI: 10.1039/d1cc01795k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of methods for amide bond formation without recourse to typical condensation reagents has become an emerging research area and has been actively explored in the past quarter century. Inspired by the structure of vitamin B12, we have developed a metal-templated macrolactamisation that generates a new wave towards classical macrolactam synthesis. Further, distinct from the extensively used methods with condensation reagents or catalysts based on catalyst/reagent control our metal-catalysed methods based on substrate control can effectively address long-standing challenges such as racemisation in the field of peptide chemistry. In addition, the substrate-controlled strategy demonstrates the feasibility of "remote" peptide bond-forming reaction catalysed by a metal-ligand complex. Moreover, an originally designed hydrosilane/aminosilane system can avoid not only racemisation but also unnecessary waste production. This feature article documents our discovery and application of our original approaches in amide bond formation.
Collapse
Affiliation(s)
- Wataru Muramatsu
- Molecular Catalyst Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan.
| | - Tomohiro Hattori
- Molecular Catalyst Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan.
| | - Hisashi Yamamoto
- Molecular Catalyst Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan.
| |
Collapse
|
28
|
Kharchenko SH, Iampolska AD, Radchenko DS, Vashchenko BV, Voitenko ZV, Grygorenko OO. A Diversity‐Oriented Approach to Large Libraries of Artificial Macrocycles. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Anna D. Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Bohdan V. Vashchenko
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Zoia V. Voitenko
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| |
Collapse
|
29
|
Maharani R, Napitupulu OI, Dirgantara JM, Hidayat AT, Sumiarsa D, Harneti D, Supratman U, Fukase K. Synthesis of cyclotetrapeptide analogues of c-PLAI and evaluation of their antimicrobial properties. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201822. [PMID: 33959342 PMCID: PMC8074941 DOI: 10.1098/rsos.201822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Antimicrobial peptides (AMPs) are interesting compounds owing to their ability to kill several pathogens. In order to identify new AMPs, c-PLAI analogues were synthesized and evaluated together with their linear precursors for their antimicrobial properties against two Gram-positive bacteria (Staphylococcus aureus and Bacillus cereus), two Gram-negative bacteria (Escherichia coli and Klebsiella pneumoniae), and two fungal strains (Candida albicans and Trichophyton mentagrophytes). The new c-PLAI analogues were prepared through a combination of solid- and solution-phase syntheses, as previously employed for the synthesis of c-PLAI. The antimicrobial activity tests showed that the synthetic parent peptide c-PLAI was inactive or weakly active towards the bioindicators employed in the assay. The tests also indicated that cyclic c-PLAI analogues possessed enhanced antimicrobial properties against most of the bacteria and fungi tested. Furthermore, this study revealed that analogues containing cationic lysine residues displayed the highest activity towards most bioindicators. A combination of lysine and aromatic residues yielded analogues with broad-spectrum antimicrobial properties.
Collapse
Affiliation(s)
- Rani Maharani
- Laboratorium Sentral, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
| | - Orin Inggriani Napitupulu
- Laboratorium Sentral, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
| | - Jelang M. Dirgantara
- Laboratorium Sentral, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
| | - Ace Tatang Hidayat
- Laboratorium Sentral, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
| | - Dadan Sumiarsa
- Laboratorium Sentral, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
| | - Desi Harneti
- Laboratorium Sentral, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
| | - Unang Supratman
- Laboratorium Sentral, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Jatinangor, Kabupaten Sumedang, 45363 West Java, Indonesia
| | - Koichi Fukase
- Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
30
|
Matsuda K, Fujita K, Wakimoto T. PenA, a penicillin-binding protein-type thioesterase specialized for small peptide cyclization. J Ind Microbiol Biotechnol 2021; 48:6169712. [PMID: 33713128 PMCID: PMC9113502 DOI: 10.1093/jimb/kuab023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/19/2021] [Indexed: 12/31/2022]
Abstract
Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified group of peptide cyclases that catalyze head-to-tail macrolactamization of nonribosomal peptides. PenA, a new member of this group, is involved in the biosyntheses of cyclic pentapeptides. In this study, we demonstrated the enzymatic activity of PenA in vitro, and analyzed its substrate scope with a series of synthetic substrates. A comparison of the reaction profiles between PenA and SurE, a representative PBP-type TE, showed that PenA is more specialized for small peptide cyclization. A computational model provided a possible structural rationale for the altered specificity for substrate chain lengths.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Kei Fujita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| |
Collapse
|
31
|
Chen Z, Nie XD, Sun JT, Yang AM, Wei BG. Zn(OTf) 2-catalyzed hydroamination of ynamides with aromatic amines. Org Biomol Chem 2021; 19:2492-2501. [PMID: 33656504 DOI: 10.1039/d0ob02603d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Zn(OTf)2-catalyzed hydroamination of ynamides 2a-2l with aromatic amines 1a-1r was developed. This protocol features broad substrate scope of aromatic amines, good functional group tolerance for ynamides, and excellent regioselectivities. As a result, a variety of substituted amidine compounds 3aa-3oa, 3ab-3al and 3pa-3rk were prepared in moderate to excellent yields and with high regioselectivities.
Collapse
Affiliation(s)
- Zhuo Chen
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | | | | | | | | |
Collapse
|
32
|
Nie XD, Han XL, Sun JT, Si CM, Wei BG, Lin GQ. Nickel-Catalyzed Regioselective Hydroamination of Ynamides with Secondary Amines. J Org Chem 2021; 86:3433-3443. [DOI: 10.1021/acs.joc.0c02807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiao-Di Nie
- School of Pharmacy and Institutes of Biomedical Sciences, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Xiao-Li Han
- School of Pharmacy and Institutes of Biomedical Sciences, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jian-Ting Sun
- School of Pharmacy and Institutes of Biomedical Sciences, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Chang-Mei Si
- School of Pharmacy and Institutes of Biomedical Sciences, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Bang-Guo Wei
- School of Pharmacy and Institutes of Biomedical Sciences, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Guo-Qiang Lin
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| |
Collapse
|
33
|
Conte M, Fontana E, Nebbioso A, Altucci L. Marine-Derived Secondary Metabolites as Promising Epigenetic Bio-Compounds for Anticancer Therapy. Mar Drugs 2020; 19:md19010015. [PMID: 33396307 PMCID: PMC7824531 DOI: 10.3390/md19010015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022] Open
Abstract
Sessile organisms such as seaweeds, corals, and sponges continuously adapt to both abiotic and biotic components of the ecosystem. This extremely complex and dynamic process often results in different forms of competition to ensure the maintenance of an ecological niche suitable for survival. A high percentage of marine species have evolved to synthesize biologically active molecules, termed secondary metabolites, as a defense mechanism against the external environment. These natural products and their derivatives may play modulatory roles in the epigenome and in disease-associated epigenetic machinery. Epigenetic modifications also represent a form of adaptation to the environment and confer a competitive advantage to marine species by mediating the production of complex chemical molecules with potential clinical implications. Bioactive compounds are able to interfere with epigenetic targets by regulating key transcriptional factors involved in the hallmarks of cancer through orchestrated molecular mechanisms, which also establish signaling interactions of the tumor microenvironment crucial to cancer phenotypes. In this review, we discuss the current understanding of secondary metabolites derived from marine organisms and their synthetic derivatives as epigenetic modulators, highlighting advantages and limitations, as well as potential strategies to improve cancer treatment.
Collapse
|
34
|
Li H, Ren J, Li J, Zhang Z, Chang N, Qin C. Greener liquid-phase synthesis and the ACE inhibitory structure-activity relationship of an anti-SARS octapeptide. Org Biomol Chem 2020; 18:8433-8442. [PMID: 33057549 DOI: 10.1039/d0ob01948h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A high-efficiency strategy for resin-free and large scale liquid phase synthesis of the anti-SARS octapeptide AVLQSGFR is described. Herein, tri(4'-diphenylphosphonyloxylbenzoyl phenyl)phosphate (TDPBP) derivatives were designed as C-terminal supports to aid octapeptide intermediate purification without the need for chromatographic separation. Furthermore, the ACE inhibitory structure-activity relationship (SAR) of the anti-SARS octapeptide and its alanine-scanning analogues was systematically studied by in vitro assay and 3D-QSAR via molecular docking. This paper provides a new strategy for the development of peptide-based drugs. Simultaneously, a study on the ACE inhibition and structure-activity relationship of the anti-SARS octapeptide also lays a foundation for further understanding how the anti-SARS octapeptide acts as an ACE inhibitor.
Collapse
Affiliation(s)
- Haidi Li
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Jin Ren
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Junyou Li
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Zixin Zhang
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Ninghui Chang
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Chuanguang Qin
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| |
Collapse
|
35
|
Chen S, Ruan Y, Lu JL, Hunter L, Hu XG. Diastereoselective synthesis and conformational analysis of 4,5-difluoropipecolic acids. Org Biomol Chem 2020; 18:8192-8198. [PMID: 33030197 DOI: 10.1039/d0ob01811b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Stereoselectively-fluorinated analogs of pipecolic acid have been investigated through a combined theoretical and experimental approach. Three of the four possible diastereoisomers of 4,5-difluoropipecolic acid were successfully synthesized via deoxyfluorination chemistry, navigating a complex reaction network that included neighboring group participation, rearrangement, and elimination pathways. A DFT-based conformational study, supported by NMR J-based analysis, revealed that the different diastereoisomers of 4,5-difluoropipecolic acid preferentially adopt different puckers of the six-membered ring. These findings could have future relevance for the conformational control of biologically active peptides.
Collapse
Affiliation(s)
- Suo Chen
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Yao Ruan
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Ji-Liang Lu
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia.
| | - Xiang-Guo Hu
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China. and Key Laboratory of Small Functional Organic Molecules, Jiangxi Normal University, Nanchang, 330022, P. R. China
| |
Collapse
|
36
|
Avila-Ortiz CG, Juaristi E. Novel Methodologies for Chemical Activation in Organic Synthesis under Solvent-Free Reaction Conditions. Molecules 2020; 25:E3579. [PMID: 32781678 PMCID: PMC7464687 DOI: 10.3390/molecules25163579] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
One central challenge for XXI century chemists is the development of sustainable processes that do not represent a risk either to humanity or to the environment. In this regard, the search for more efficient and clean alternatives to achieve the chemical activation of molecules involved in chemical transformations has played a prominent role in recent years. The use of microwave or UV-Vis light irradiation, and mechanochemical activation is already widespread in many laboratories. Nevertheless, an additional condition to achieve "green" processes comes from the point of view of so-called atom economy. The removal of solvents from chemical reactions generally leads to cleaner, more efficient and more economical processes. This review presents several illustrative applications of the use of sustainable protocols in the synthesis of organic compounds under solvent-free reaction conditions.
Collapse
Affiliation(s)
- Claudia Gabriela Avila-Ortiz
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. IPN 2508, 07360 Ciudad de México, Mexico
| | - Eusebio Juaristi
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. IPN 2508, 07360 Ciudad de México, Mexico
- El Colegio Nacional, Donceles 104, Centro Histórico, 06020 Ciudad de México, Mexico
| |
Collapse
|
37
|
Jwad R, Weissberger D, Hunter L. Strategies for Fine-Tuning the Conformations of Cyclic Peptides. Chem Rev 2020; 120:9743-9789. [PMID: 32786420 DOI: 10.1021/acs.chemrev.0c00013] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.
Collapse
Affiliation(s)
- Rasha Jwad
- Department of Chemistry, College of Science, Al-Nahrain University, Baghdad, Iraq
| | - Daniel Weissberger
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
| | - Luke Hunter
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
| |
Collapse
|
38
|
Gordon CP. Synthetic strategies to access staphylococcus auto-inducing peptides as quorum sensing modulators. Org Biomol Chem 2020; 18:379-390. [PMID: 31844862 DOI: 10.1039/c9ob02038a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The accessory gene regulator (agr) quorum-sensing system is arguably the most important regulator of staphylococcus virulence and has been the focus of tremendous interest in the development of effective therapies for pathogenic bacterial infections. With regards to chemotherapeutic based strategies, the significant proportion of currently reported agr-system modulating molecules are mimics of the native ArgC substrate, which is a thioester-based macrocyclic peptide know as the auto-inducing peptide. Over the past two decades, more than two-hundred synthetic analogues have been reported. This review traces the development of the synthetic strategies employed to synthesise these analogues with a particular focus on macrocyclisation. At present these synthetic approaches can be clustered into five broad categories (1) solution-phase cyclisation, (2) immobilised carbodiimide assisted cyclisation, (3) concomitant on-resin cleavage and macrocyclisation, (4) Boc-compatible chemoselective thioesterification, and (5) Fmoc-compatible chemoselective thioesterification. The advantages and limitation provided by each of the approaches are compared and contrasted with a view towards potential reaction scale-up.
Collapse
Affiliation(s)
- Christopher P Gordon
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith South DC, NSW 2751, Australia.
| |
Collapse
|
39
|
Serra G, Posada L, Hojo H. On-resin synthesis of cyclic peptides via tandem N-to-S acyl migration and intramolecular thiol additive-free native chemical ligation. Chem Commun (Camb) 2020; 56:956-959. [DOI: 10.1039/c9cc07783a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A novel methodology for the synthesis of cyclic peptides by on-resin intramolecular native chemical ligation (NCL) assisted by N-ethylcysteine using Fmoc/SPPS is described.
Collapse
Affiliation(s)
- Gloria Serra
- Química Farmacéutica
- Departamento de Química Orgánica
- Facultad de Química
- Universidad de la República
- Montevideo
| | - Laura Posada
- Química Farmacéutica
- Departamento de Química Orgánica
- Facultad de Química
- Universidad de la República
- Montevideo
| | - Hironobu Hojo
- Institute for Protein Research
- Osaka University
- Yamadaoka
- Suita-shi
- Japan
| |
Collapse
|