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You Y, Kong H, Li C, Gu Z, Ban X, Li Z. Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes. Biotechnol Adv 2024; 73:108365. [PMID: 38677391 DOI: 10.1016/j.biotechadv.2024.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Carbohydrate binding modules (CBMs) are independent non-catalytic domains widely found in carbohydrate-active enzymes (CAZymes), and they play an essential role in the substrate binding process of CAZymes by guiding the appended catalytic modules to the target substrates. Owing to their precise recognition and selective affinity for different substrates, CBMs have received increasing research attention over the past few decades. To date, CBMs from different origins have formed a large number of families that show a variety of substrate types, structural features, and ligand recognition mechanisms. Moreover, through the modification of specific sites of CBMs and the fusion of heterologous CBMs with catalytic domains, improved enzymatic properties and catalytic patterns of numerous CAZymes have been achieved. Based on cutting-edge technologies in computational biology, gene editing, and protein engineering, CBMs as auxiliary components have become portable and efficient tools for the evolution and application of CAZymes. With the aim to provide a theoretical reference for the functional research, rational design, and targeted utilization of novel CBMs in the future, we systematically reviewed the function-related characteristics and potentials of CAZyme-derived CBMs in this review, including substrate recognition and binding mechanisms, non-catalytic contributions to enzyme performances, module modifications, and innovative applications in various fields.
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Affiliation(s)
- Yuxian You
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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2
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Muramatsu W, Yamamoto H. An economical approach for peptide synthesis via regioselective C-N bond cleavage of lactams. Chem Sci 2022; 13:6309-6315. [PMID: 35733900 PMCID: PMC9159104 DOI: 10.1039/d2sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/21/2022] [Indexed: 11/21/2022] Open
Abstract
An economical, solvent-free, and metal-free method for peptide synthesis via C-N bond cleavage using lactams has been developed. The method not only eliminates the need for condensation agents and their auxiliaries, which are essential for conventional peptide synthesis, but also exhibits high atom economy. The reaction is versatile because it can tolerate side chains bearing a range of functional groups, affording up to >99% yields of the corresponding peptides without racemisation or polymerisation. Moreover, the developed strategy enables peptide segment coupling, providing access to a hexapeptide that occurs as a repeat sequence in spider silk proteins.
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Affiliation(s)
- Wataru Muramatsu
- Peptide Research Center, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
| | - Hisashi Yamamoto
- Peptide Research Center, Chubu University 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
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3
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Poonia BK, Sidhu A, Sharma AB. Cyclo(l-proline-l-serine) Dipeptide Suppresses Seed Borne Fungal Pathogens of Rice: Altered Cellular Membrane Integrity of Fungal Hyphae and Seed Quality Benefits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2160-2168. [PMID: 35142498 DOI: 10.1021/acs.jafc.1c07659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Five proline-containing diketopiperazines (Pro-DKPs) produced by antagonistic microorganisms as secondary metabolites were selected and synthesized under laboratory conditions. Out of five synthesized Pro-DKPs, cyclo(l-Pro-l-Ser) (DKP-6) revealed the best inhibition of fungal pathogens (Fusarium verticillioides and Fusarium fujikuroi) of rice under in vitro conditions with effective doses lower than standard fungicide carbendazim. DKP-6 induced stress on the fungal cell membrane integrity, which was revealed by calcofluor white and propidium iodide assays, endorsed by ultra-microscopic details and soluble protein leakage assays. In vivo seed treatment of infested rice seeds with DKP-6 at 2000 μg/mL for 10 h of seed treatment inflicted best reduction in seed rot and seedling blight with respect to control and carbendazim. Significant enhancement in seedling quality parameters were also observed. The work presented the strong influence of cyclo(l-Pro-l-Ser) as a mycocidal seed treatment agent better than synthetic toxic fungicides for rice.
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Affiliation(s)
| | - Anjali Sidhu
- Department of Soil Science, Punjab Agricultural University, Ludhiana 141004, India
| | - Anju Bala Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India
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4
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Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Biomolecules 2021; 11:1515. [PMID: 34680148 PMCID: PMC8533947 DOI: 10.3390/biom11101515] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Istvan Toth
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Sherif Elnagdy
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Maha AlKhazindar
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
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Zhang L, Feng LL, Wang GF, Yang QL, Fu XZ, Li Z, Liu M, Kou LJ, Xu B, Xie ZP, Zhang SM, Guo L. Strepyrazinone, a tricyclic diketopiperazine derivative with cytotoxicity from a marine-derived actinobacterium. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2021; 23:968-974. [PMID: 32819169 DOI: 10.1080/10286020.2020.1801649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Strepyrazinone (1), a tricyclic diketopiperazine derivative with a carbon skeleton unprecedented in natural products, was isolated from the marine-derived Streptomyces sp. B223. Its structure was elucidated by spectroscopic analyses and electronic circular dichroism calculation. Compound 1 showed cytotoxic activity against HCT-116 cancer cell lines with an IC50 value of 0.34 µM.
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Affiliation(s)
- Lu Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Ling-Ling Feng
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Guang-Fei Wang
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Qiao-Li Yang
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Xin-Zhen Fu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Zhi Li
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Ming Liu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Li-Juan Kou
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Bo Xu
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Ze-Ping Xie
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
- Shandong International Biotechnology Park, Yantai 264670, China
| | - Shu-Min Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
- Shandong International Biotechnology Park, Yantai 264670, China
| | - Lin Guo
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
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6
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Wu C, Murugan SP, Wang Y, Pan H, Sun B, Lin Y, Fatimah S, Chang AHH, Chen C, Lee G. Synthesis of Indoline‐Fused 2,5‐Diketopiperazine Scaffolds
via
Ugi‐4CR in the Basic Mediated Tandem Consecutive Cyclization. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Chih‐Yu Wu
- Department of Nursing Tzu Chi University of Science and Technology Hualien 970302 Taiwan
| | | | - Yu‐Wei Wang
- Department of Chemistry National Dong Hwa University Shoufeng Hualien 974301 Taiwan
| | - Hao‐Wei Pan
- Department of Chemistry National Dong Hwa University Shoufeng Hualien 974301 Taiwan
| | - Bing‐Jian Sun
- Department of Chemistry National Dong Hwa University Shoufeng Hualien 974301 Taiwan
| | - Yu‐Ting Lin
- Department of Chemistry National Dong Hwa University Shoufeng Hualien 974301 Taiwan
| | - Siti Fatimah
- Department of Chemistry National Dong Hwa University Shoufeng Hualien 974301 Taiwan
| | - Agnes H. H. Chang
- Department of Chemistry National Dong Hwa University Shoufeng Hualien 974301 Taiwan
| | - Chinpiao Chen
- Department of Nursing Tzu Chi University of Science and Technology Hualien 970302 Taiwan
- Department of Chemistry National Dong Hwa University Shoufeng Hualien 974301 Taiwan
| | - Gene‐Hsian Lee
- Instrumentation Center National Taiwan University Taipei 10617 Taiwan
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Balachandra C, Padhi D, Govindaraju T. Cyclic Dipeptide: A Privileged Molecular Scaffold to Derive Structural Diversity and Functional Utility. ChemMedChem 2021; 16:2558-2587. [PMID: 33938157 DOI: 10.1002/cmdc.202100149] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/11/2022]
Abstract
Cyclic dipeptides (CDPs) are the simplest form of cyclic peptides with a wide range of applications from therapeutics to biomaterials. CDP is a versatile molecular platform endowed with unique properties such as conformational rigidity, intermolecular interactions, structural diversification through chemical synthesis, bioavailability and biocompatibility. A variety of natural products with the CDP core exhibit anticancer, antifungal, antibacterial, and antiviral activities. The inherent bioactivities have inspired the development of synthetic analogues as drug candidates and drug delivery systems. CDP plays a crucial role as conformation and molecular assembly directing core in the design of molecular receptors, peptidomimetics and fabrication of functional material architectures. In recent years, CDP has rapidly become a privileged scaffold for the design of advanced drug candidates, drug delivery agents, bioimaging, and biomaterials to mitigate numerous disease conditions. This review describes the structural diversification and multifarious biomedical applications of the CDP scaffold, discusses challenges, and provides future directions for the emerging field.
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Affiliation(s)
- Chenikkayala Balachandra
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bangalore, 560064, India
| | - Dikshaa Padhi
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bangalore, 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bangalore, 560064, India
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8
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Qader MM, Hamed AA, Soldatou S, Abdelraof M, Elawady ME, Hassane ASI, Belbahri L, Ebel R, Rateb ME. Antimicrobial and Antibiofilm Activities of the Fungal Metabolites Isolated from the Marine Endophytes Epicoccum nigrum M13 and Alternaria alternata 13A. Mar Drugs 2021; 19:md19040232. [PMID: 33924262 PMCID: PMC8074750 DOI: 10.3390/md19040232] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 01/15/2023] Open
Abstract
Epicotripeptin (1), a new cyclic tripeptide along with four known cyclic dipeptides (2-5) and one acetamide derivative (6) were isolated from seagrass-associated endophytic fungus Epicoccum nigrum M13 recovered from the Red Sea. Additionally, two new compounds, cyclodidepsipeptide phragamide A (7) and trioxobutanamide derivative phragamide B (8), together with eight known compounds (9-16), were isolated from plant-derived endophyte Alternaria alternata 13A collected from a saline lake of Wadi El Natrun depression in the Sahara Desert. The structures of the isolated compounds were determined based on the 1D and 2D NMR spectroscopic data, HRESIMS data, and a comparison with the reported literature. The absolute configurations of 1 and 7 were established by advanced Marfey's and Mosher's ester analyses. The antimicrobial screening indicated that seven of the tested compounds exhibited considerable (MIC range of 2.5-5 µg/mL) to moderate (10-20 µg/mL) antibacterial effect against the tested Gram-positive strains and moderate to weak (10-30 µg/mL) antibacterial effect against Gram-negative strains. Most of the compounds exhibited weak or no activity against the tested Gram-negative strains. On the other hand, four of the tested compounds showed considerable antibiofilm effects against biofilm forming Gram-positive and Gram-negative strains.
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Affiliation(s)
- M. Mallique Qader
- School of Computing, Engineering, & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (M.M.Q.); (A.S.I.H.)
- National Institute of Fundamental Studies, Hantana Road, Kandy 20000, Sri Lanka
| | - Ahmed A. Hamed
- National Research Centre, Microbial Chemistry Department, 33 El-Buhouth Street, Dokki, Giza 12622, Egypt; (A.A.H.); (M.A.)
| | - Sylvia Soldatou
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK;
| | - Mohamed Abdelraof
- National Research Centre, Microbial Chemistry Department, 33 El-Buhouth Street, Dokki, Giza 12622, Egypt; (A.A.H.); (M.A.)
| | - Mohamed E. Elawady
- National Research Centre, Microbial Biotechnology Department, 33 El-Buhouth Street, Dokki, Giza 12622, Egypt;
| | - Ahmed S. I. Hassane
- School of Computing, Engineering, & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (M.M.Q.); (A.S.I.H.)
- Aberdeen Royal Infirmary, Foresterhill Health Campus, Aberdeen AB25 2ZN, UK
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 2000 Neuchatel, Switzerland;
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK;
- Correspondence: (R.E.); (M.E.R.); Tel.: +44-1224-272930 (R.E.); +44-141-8483072 (M.E.R.)
| | - Mostafa E. Rateb
- School of Computing, Engineering, & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (M.M.Q.); (A.S.I.H.)
- Correspondence: (R.E.); (M.E.R.); Tel.: +44-1224-272930 (R.E.); +44-141-8483072 (M.E.R.)
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Abstract
The complexity of animal microbiomes presents challenges to defining signaling molecules within the microbial consortium and between the microbes and the host. By focusing on the binary symbiosis between Vibrio fischeri and Euprymna scolopes, we have combined genetic analysis with direct imaging to define and study small molecules in the intact symbiosis. The lifelong relationship between the Hawaiian bobtail squid Euprymna scolopes and its microbial symbiont Vibrio fischeri represents a simplified model system for studying microbiome establishment and maintenance. The bacteria colonize a dedicated symbiotic light organ in the squid, from which bacterial luminescence camouflages the host in a process termed counterillumination. The squid host hatches without its symbionts, which must be acquired from the ocean amidst a diversity of nonbeneficial bacteria, such that precise molecular communication is required for initiation of the specific relationship. Therefore it is likely there are specialized metabolites used in the light organ microenvironment to modulate these processes. To identify small molecules that may influence the establishment of this symbiosis, we used imaging mass spectrometry to analyze metabolite production in V. fischeri with altered biofilm production, which correlates directly to colonization capability in its host. “Biofilm-up” and “biofilm-down” mutants were compared to a wild-type strain, and ions that were more abundantly produced by the biofilm-up mutant were detected. Using a combination of structural elucidation and synthetic chemistry, one such signal was determined to be a diketopiperazine, cyclo(d-histidyl-l-proline). This diketopiperazine modulated luminescence in V. fischeri and, using imaging mass spectrometry, was directly detected in the light organ of the colonized host. This work highlights the continued need for untargeted discovery efforts in host-microbe interactions and showcases the benefits of the squid-Vibrio system for identification and characterization of small molecules that modulate microbiome behaviors.
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Sargolzaei M, Nikoofard H, Jorabchi MN. Quantum-Chemical ab initio Study of Side Chain pKa of Linear and Cyclic Lysine Dipeptides. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cyclic dipeptides show interesting biological activities such as antitumor, antiviral and so on. In biological systems, the bioavailability of drugs is determined by several parameters such as pKa values. In this study, we used DFT and thermodynamics cycle to determine pKa value of side chain of lysine in linear and cyclic dipeptides. All considered dipeptides were optimized using B3LYP and RMSD tool was used to compare the optimized structures. The calculated pKa values were compared with the available experimental data. Our results show that pKa of side chain of lysine increases for cyclic dipeptides compared to the linear ones. To justify the reason of increasing of pKa of cyclic dipeptides, we used NBO and AIM analyses. The analyses showed that a hydrogen bond in cyclic lysine dipeptides is responsible for increasing of pKa.
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Affiliation(s)
- Mohsen Sargolzaei
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Hossein Nikoofard
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Majid Namayandeh Jorabchi
- University of Rostock, Institute of Chemistry, Physical and Theoretical Chemistry, Albert-Einstein-Straße 21, 18059 Rostock, Germany
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11
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Madan K, Madan M, Sharma S, Paliwal S. Chitinases: Therapeutic Scaffolds for Allergy and Inflammation. ACTA ACUST UNITED AC 2020; 14:46-57. [PMID: 31934842 PMCID: PMC7509760 DOI: 10.2174/1872213x14666200114184054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/19/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022]
Abstract
Background: Chitinases are the evolutionary conserved glycosidic enzymes that are characterized by their ability to cleave the naturally abundant polysaccharide chitin. The potential role of chitinases has been identified in the manifestation of various allergies and inflammatory diseases. In recent years, chitinases inhibitors are emerging as an alluring area of interest for the researchers and scientists and there is a dire need for the development of potential and safe chitinase antagonists for the prophylaxis and treatment of several diseases. Objective: The present review expedites the role of chitinases and their inhibitors in inflammation and related disorders. Methods: At first, an exhaustive survey of literature and various patents available related to chitinases were carried out. Useful information on chitinases and their inhibitor was gathered from the authentic scientific databases namely SCOPUS, EMBASE, PUBMED, GOOGLE SCHOLAR, MEDLINE, EMBASE, EBSCO, WEB OF SCIENCE, etc. This information was further analyzed and compiled up to prepare the framework of the review article. The search strategy was conducted by using queries with key terms “ chitin”, “chitinase”, “chitotrisidase”, “acidic mammalian chitinase”, “chitinase inhibitors”, “asthma” and “chitinases associated inflammatory disorders”, etc. The patents were searched using the key terms “chitinases and uses thereof”, “chitinase inhibitors”, “chitin-chitinase associated pathological disorders” etc. from www.google.com/patents, www.freepatentsonline.com, and www.scopus.com. Results: The present review provides a vision for apprehending human chitinases and their participation in several diseases. The patents available also signify the extended role and effectiveness of chitinase inhibitors in the prevention and treatment of various diseases viz. asthma, acute and chronic inflammatory diseases, autoimmune diseases, dental diseases, neurologic diseases, metabolic diseases, liver diseases, polycystic ovary syndrome, endometriosis, and cancer. In this regard, extensive pre-clinical and clinical investigations are required to develop some novel, potent and selective drug molecules for the treatment of various inflammatory diseases, allergies and cancers in the foreseeable future. Conclusion: In conclusion, chitinases can be used as potential biomarkers in prognosis and diagnosis of several inflammatory diseases and allergies and the design of novel chitinase inhibitors may act as key and rational scaffolds in designing some novel therapeutic agents in the treatment of variety of inflammatory diseases.
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Affiliation(s)
- Kirtika Madan
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan-304022, India
| | - Mansi Madan
- Dr. Ulhas Patil Medical College and Hospital, Jalgaon- 425309, Maharashtra, India
| | - Swapnil Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan-304022, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan-304022, India
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Serratia marcescens secretes proteases and chitinases with larvicidal activity against Anopheles dirus. Acta Trop 2020; 212:105686. [PMID: 32866458 DOI: 10.1016/j.actatropica.2020.105686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/01/2023]
Abstract
Vector control, the most efficient tool to reduce mosquito-borne disease transmission, has been compromised by the rise of insecticide resistance. Recent studies suggest the potential of mosquito-associated microbiota as a source for new biocontrol agents or new insecticidal chemotypes. In this study, we identified a strain of Serratia marcescens that has larvicidal activity against Anopheles dirus, an important malaria vector in Southeast Asia. This bacterium secretes heat-labile larvicidal macromolecules when cultured under static condition at 25°C but not 37°C. Two major protein bands of approximately 55 kDa and 110 kDa were present in spent medium cultured at 25°C but not at 37°C. The Liquid Chromatography-Mass Spectrometry (LC-MS) analyses of these two protein bands identified several proteases and chitinases that were previously reported for insecticidal properties against agricultural insect pests. The treatment with protease and chitinase inhibitors led to a reduction in larvicidal activity, confirming that these two groups of enzymes are responsible for the macromolecule's toxicity. Taken together, our results suggest a potential use of these enzymes in the development of larvicidal agents against Anopheles mosquitoes.
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13
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Glycoside hydrolase family 18 chitinases: The known and the unknown. Biotechnol Adv 2020; 43:107553. [DOI: 10.1016/j.biotechadv.2020.107553] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/09/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
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14
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Yang H, Qi H, Hao Z, Shao X, Liu T, Yang Q, Qian X. Thiazolylhydrazone dervatives as inhibitors for insect N-acetyl-β-d-hexosaminidase and chitinase. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.11.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Sargolzaei M, Jorabchi MN. Cyclization Effect on pKa of the Side Chain of Aspartic Acid in Dipeptides: A DFT Study. LETT ORG CHEM 2020. [DOI: 10.2174/1570178616666191019124709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cyclic dipeptides are very important compounds that have a wide range of applications in
pharmaceutical chemistry and life sciences. In the current work, the acidity of the side chain of aspartic
acid was calculated for various linear and a cyclic dipeptide. pKa values were derived using the thermodynamics
cycle and DFT/B3LYP approach. The obtained pKa values show strong acidity for cyclic
with respect to linear dipeptides. We found an intramolecular hydrogen bond in cyclic dipeptide structure,
which can be used to justify the increasing acidity of the side chain of Asp as compared to linear
structures.
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Affiliation(s)
- Mohsen Sargolzaei
- Department of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Majid Namayandeh Jorabchi
- University of Rostock, Institute of Chemistry, Physical and Theoretical Chemistry, Albert-Einstein-Straße 21, 18059 Rostock, Germany
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16
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Wei X, Feng C, Wang SY, Zhang DM, Li XH, Zhang CX. New Indole Diketopiperazine Alkaloids from Soft Coral-Associated Epiphytic Fungus Aspergillus sp. EGF 15-0-3. Chem Biodivers 2020; 17:e2000106. [PMID: 32212241 DOI: 10.1002/cbdv.202000106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/24/2020] [Indexed: 11/09/2022]
Abstract
Three new indole diketopiperazine alkaloids, 11-methylneoechinulin E and variecolorin M, and (+)-variecolorin G, along with 12 known analogs, were isolated from a soft coral-associated epiphytic fungus Aspergillus sp. EGF 15-0-3. The structures of the new compounds were unambiguously established by extensive spectroscopic analyses including HR-ESI-MS, 1D and 2D NMR spectroscopy and optical rotation measurements. The absolute configurations of (+)- and (-)-variecolorin G were determined by experimental and quantum-chemical ECD investigations and single-crystal X-ray diffraction analysis. Variecolorin G is a pair of enantiomeric mixtures with a ratio of 1 : 2. Moreover, (+)-neoechinulin A is firstly reported as a natural product. The cytotoxic activities of all the isolated compounds against NCI-H1975 gefitinib resistance (NCI-H1975/GR) cell lines were preliminarily evaluated by MTT method.
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Affiliation(s)
- Xia Wei
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Chan Feng
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Si-Yu Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Dong-Mei Zhang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China
| | - Xiao-Hui Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Cui-Xian Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
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17
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Ge Y, Han Z, Wang Z, Ding K. Ir-Catalyzed Double Asymmetric Hydrogenation of 3,6-Dialkylidene-2,5-diketopiperazines for Enantioselective Synthesis of Cyclic Dipeptides. J Am Chem Soc 2019; 141:8981-8988. [PMID: 31079460 DOI: 10.1021/jacs.9b02920] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An Ir/spiro[4,4]-1,6-nonadiene-based phosphine-oxazoline ligand (SpinPHOX) complex-catalyzed double asymmetric hydrogenation of 3,6-dialkylidene-1,4-dimethylpiperazine-2,5-diones has been developed, providing efficient and practical access to a wide variety of chiral 3,6-disubstituted-2,5-diketopiperazines in high yields with exclusive cis-diastereo- and excellent enantioselectivities (>99% de, up to 98% ee). The synthetic utilities of the protocol have been demonstrated in a gram scale synthesis of 6a and efficient construction of chiral products 8, 14, and 17 as well as a 2-butenyl-bridged bicyclic diketopiperazine 10 and hydroxydiketopiperazine 11. With an analogous achiral Ir catalyst, the hydrogenation of enantiopure monohydrogenated intermediate 7a gave cis-6a as the only product, indicating that the second-step hydrogenation of the titled transformation is a chiral substrate controlled process. The reaction profile study for asymmetric hydrogenation (AH) of 5a revealed that the concentration of the monohydrogenation intermediate 7a remained at a low level (<8%) during the course of hydrogenation. The hydrogenation of 5a to 6a proceeded significantly faster than that of its half-hydrogenated intermediate ( S)-7a, indicating that the titled reaction involves primarily a processive mechanism, in which a single catalyst molecule performs consecutive hydrogenation of the two C═C double bonds in substrate 5a without dissociation of the partially reduced 7a. The present protocol represents a rare example of asymmetric catalytic consecutive hydrogenation of heterocycles and provides an alternative way for efficient construction of cyclic dipeptides.
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Affiliation(s)
- Yao Ge
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhaobin Han
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Zheng Wang
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Kuiling Ding
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Nankai University , Tianjin 300071 , China
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18
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Synthesis, homology modeling, molecular docking, dynamics, and antifungal screening of new 4-hydroxycoumarin derivatives as potential chitinase inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.11.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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19
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Uprety R, Váradi A, Allaoa A, Redel-Traub GN, Palmer TC, Feinberg EN, Ferris AC, Pande VS, Pasternak GW, Majumdar S. Synthesis of spiro-2,6-dioxopiperazine and spiro-2,6-dioxopyrazine scaffolds using amino acids in a three-component reaction to generate potential Sigma-1 (σ 1) receptor selective ligands. Eur J Med Chem 2019; 164:241-251. [PMID: 30597325 PMCID: PMC6361672 DOI: 10.1016/j.ejmech.2018.12.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 01/04/2023]
Abstract
A library-friendly approach to generate new scaffolds is decisive for the development of molecular probes, drug like molecules and preclinical entities. Here, we present the design and synthesis of novel heterocycles with spiro-2,6-dioxopiperazine and spiro-2,6-pyrazine scaffolds through a three-component reaction using various amino acids, ketones, and isocyanides. Screening of select compounds over fifty CNS receptors including G-protein coupled receptors (GPCRs), ion channels, transporters, and enzymes through the NIMH psychoactive drug screening program indicated that a novel spiro-2,6-dioxopyrazine scaffold, UVM147, displays high binding affinity at sigma-1 (σ1) receptor in the nanomolar range. In addition, molecular docking of UVM147 at the human σ1 receptor have shown that it resides in the same binding site that was occupied by the ligand 4-IBP used to obtain a crystal structure of the human sigma-1 (σ1) receptor.
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Affiliation(s)
- Rajendra Uprety
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA
| | - András Váradi
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA
| | - Abdullah Allaoa
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA
| | - Gabriel N Redel-Traub
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA
| | - Travis C Palmer
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA
| | - Evan N Feinberg
- Biophysics Program and Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Alex C Ferris
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Vijay S Pande
- Biophysics Program and Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Gavril W Pasternak
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA
| | - Susruta Majumdar
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, NY, USA; Center for Clinical Pharmacology, St. Louis College of Pharmacy and Washington University School of Medicine, St. Louis, MO, USA.
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20
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Xi YK, Zhang H, Li RX, Kang SY, Li J, Li Y. Total Synthesis of Spirotryprostatins through Organomediated Intramolecular Umpolung Cyclization. Chemistry 2019; 25:3005-3009. [DOI: 10.1002/chem.201806411] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yong-Kai Xi
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Rui-Xi Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Shi-Yuan Kang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Jin Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Yan Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
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21
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Simon G, Bérubé C, Voyer N, Grenier D. Anti-biofilm and anti-adherence properties of novel cyclic dipeptides against oral pathogens. Bioorg Med Chem 2018; 27:2323-2331. [PMID: 30528685 DOI: 10.1016/j.bmc.2018.11.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/14/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022]
Abstract
Microorganisms embedded in a biofilm are significantly more resistant to antimicrobial agents and the defences of the human immune system, than their planktonic counterpart. Consequently, compounds that can inhibit biofilm formation are of great interest for novel therapeutics. In this study, a screening approach was used to identify novel cyclic dipeptides that have anti-biofilm activity against oral pathogens. Five new active compounds were identified that prevent biofilm formation by the cariogenic bacterium Streptococcus mutans and the pathogenic fungus Candida albicans. These compounds also inhibit the adherence of microorganisms to a hydroxylapatite surface. Further investigations were conducted on these compounds to establish the structure-activity relationship, and it was deduced that the common cleft pattern is required for these molecules to act effectively against biofilms.
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Affiliation(s)
- Gaëlle Simon
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, 2420, rue de la Terrasse, Québec, QC G1V 0A6, Canada; Département de Chimie and PROTEO, Université Laval, Québec, QC G1V 0A6, Canada
| | - Christopher Bérubé
- Département de Chimie and PROTEO, Université Laval, Québec, QC G1V 0A6, Canada
| | - Normand Voyer
- Département de Chimie and PROTEO, Université Laval, Québec, QC G1V 0A6, Canada. normand.voyer.@chm.ulaval.ca
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, 2420, rue de la Terrasse, Québec, QC G1V 0A6, Canada.
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22
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Synthesis and characterization of novel biodegradable water dispersed poly(ether-urethane)s and their MWCNT-AS nanocomposites functionalized with aspartic acid as dispersing agent. IRANIAN POLYMER JOURNAL 2018. [DOI: 10.1007/s13726-018-0655-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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23
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24
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Elyas YYA, Miyatani K, Bito T, Uraji M, Hatanaka T, Shimizu K, Arima J. Active site pocket of Streptomycesd-stereospecific amidohydrolase has functional roles in aminolysis activity. J Biosci Bioeng 2018; 126:293-300. [PMID: 29628267 DOI: 10.1016/j.jbiosc.2018.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 11/19/2022]
Abstract
d-Stereospecific amidohydrolase from Streptomyces sp. 82F2 (DAH) recognizes d-amino acyl ester derivatives as substrates and catalyzes hydrolysis and aminolysis to yield d-amino acids and d-amino acyl peptides or amide derivatives, respectively. Crystallographic analysis has revealed that DAH possesses a large cavity with a small pocket at the bottom. Because the pocket is close to the catalytic center and is thought to interact with substrates, we examined the function of the eight residues that form the pocket in terms of substrate recognition and aminolysis via mutational analysis. Formation of the acyl-enzyme intermediate and catalysis of aminolysis by DAH were changed by substitutions of selected residues with Ala. In particular, I338A DAH exhibited a significant increase in the condensation product of Ac-d-Phe methyl ester and 1,8-diaminooctane (Ac-d-Phe-1,8-diaminooctane) compared with the wild-type DAH. A similar effect was observed by the mutation of Ile338 to Gly and Ser. The pocket shapes and local flexibility of the mutants I338G, I338A, and I338S are thought to resemble each other. Thus, changes in the shape and local flexibility of the pocket of DAH by mutation presumably alter substrate recognition for aminolysis.
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Affiliation(s)
| | - Kazusa Miyatani
- Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan
| | - Tomohiro Bito
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Misugi Uraji
- Research Institute for Biological Sciences (RIBS), Okayama 716-1241, Japan
| | - Tadashi Hatanaka
- Research Institute for Biological Sciences (RIBS), Okayama 716-1241, Japan
| | - Katsuhiko Shimizu
- Division of Regional Contribution and Lifelong Learning, Organization of Regional Industrial-Academic Cooperation, Tottori University, 4-101 Koyama-minami, Tottori 680-8550, Japan
| | - Jiro Arima
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
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25
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Kwak MK, Liu R, Kang SO. Antimicrobial activity of cyclic dipeptides produced by Lactobacillus plantarum LBP-K10 against multidrug-resistant bacteria, pathogenic fungi, and influenza A virus. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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26
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Fisher CL, Resnick RJ, De S, Acevedo LA, Lu KP, Schroeder FC, Nicholson LK. Cyclic cis-Locked Phospho-Dipeptides Reduce Entry of AβPP into Amyloidogenic Processing Pathway. J Alzheimers Dis 2018; 55:391-410. [PMID: 27662285 DOI: 10.3233/jad-160051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cis/trans isomerization of X-Pro peptide bonds in proteins in some instances acts as a molecular switch in biological pathways. Our prior work suggests that the cis isomer of the phospho-Thr668-Pro669 motif, located in the cytoplasmic domain of the amyloid-β protein precursor (AβPP), is correlated with an increase in amyloidogenic processing of AβPP and production of amyloid-beta (Aβ), the neurotoxic peptide fragment in Alzheimer's disease (AD). We designed a 100% cis-locked cyclic dipeptide composed of cyclized phospho-Thr-Pro (pCDP) as a mimic for this putative pathological conformation, and three phosphate-blocked derivatives (pCDP-diBzl, pCDP-Bzl, and pCDP-diPOM). Two H4 neuroglioma cell lines were established as AD cell models for use in testing these compounds: H4-AβPP695 for stable overexpression of wild-type AβPP695, and H4-BACE1 for stable overexpression of β-site AβPP cleaving enzyme-1 (BACE1). The level of the secreted AβPP fragment resulting from BACE1 activity, sAβPPβ, served as a key proxy for amyloidogenic processing, since cleavage of AβPP by BACE1 is a requisite first step in Aβ production. Of the compounds tested, pCDP-diBzl decreased sAβPPβ levels in both cell lines, while pCDP-diPOM decreased sAβPPβ levels in only H4-BACE1 cells, all with similar dose-dependences and patterns of proteolytic AβPP fragments. Enzymatic assays showed that none of the pCDP derivatives directly inhibit BACE1 catalytic activity. These results suggest a model in which pCDP-diBzl and pCDP-diPOM act at a common point to inhibit entry of AβPP into the amyloidogenic AβPP processing pathway but through different targets, and provide important insights for the development of novel AD therapeutics.
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Affiliation(s)
- Carolyn L Fisher
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Ross J Resnick
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Soumya De
- School of Bio Science, Indian Institute of Technology, Kharagpur, WB, India
| | - Lucila A Acevedo
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Kun Ping Lu
- Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Linda K Nicholson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
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27
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Jida M, Ballet S. An Efficient One-Pot Synthesis of Chiral N-Protected 3-Substituted (Diketo)piperazines via Ugi-4CR/De-Boc/Cyclization Process. ChemistrySelect 2018. [DOI: 10.1002/slct.201702943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mouhamad Jida
- Research Group of Organic Chemistry; Departments of Chemistry and Bioengineering Sciences; Vrije Universiteit Brussel; Pleinlaan 2 B-1050 Brussels Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry; Departments of Chemistry and Bioengineering Sciences; Vrije Universiteit Brussel; Pleinlaan 2 B-1050 Brussels Belgium
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28
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Nelson TM, Borgogna JC, Michalek RD, Roberts DW, Rath JM, Glover ED, Ravel J, Shardell MD, Yeoman CJ, Brotman RM. Cigarette smoking is associated with an altered vaginal tract metabolomic profile. Sci Rep 2018; 8:852. [PMID: 29339821 PMCID: PMC5770521 DOI: 10.1038/s41598-017-14943-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/18/2017] [Indexed: 02/08/2023] Open
Abstract
Cigarette smoking has been associated with both the diagnosis of bacterial vaginosis (BV) and a vaginal microbiota lacking protective Lactobacillus spp. As the mechanism linking smoking with vaginal microbiota and BV is unclear, we sought to compare the vaginal metabolomes of smokers and non-smokers (17 smokers/19 non-smokers). Metabolomic profiles were determined by gas and liquid chromatography mass spectrometry in a cross-sectional study. Analysis of the 16S rRNA gene populations revealed samples clustered into three community state types (CSTs) ---- CST-I (L. crispatus-dominated), CST-III (L. iners-dominated) or CST-IV (low-Lactobacillus). We identified 607 metabolites, including 12 that differed significantly (q-value < 0.05) between smokers and non-smokers. Nicotine, and the breakdown metabolites cotinine and hydroxycotinine were substantially higher in smokers, as expected. Among women categorized to CST-IV, biogenic amines, including agmatine, cadaverine, putrescine, tryptamine and tyramine were substantially higher in smokers, while dipeptides were lower in smokers. These biogenic amines are known to affect the virulence of infective pathogens and contribute to vaginal malodor. Our data suggest that cigarette smoking is associated with differences in important vaginal metabolites, and women who smoke, and particularly women who are also depauperate for Lactobacillus spp., may have increased susceptibilities to urogenital infections and increased malodor.
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Affiliation(s)
- T M Nelson
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, USA
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - J C Borgogna
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, USA
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - D W Roberts
- Department of Ecology, Montana State University, Bozeman, MT, USA
| | - J M Rath
- Department of Behavioral and Community Health, University of Maryland School of Public Health, College Park, MD, USA
- Truth Initiative, Washington DC, USA
| | - E D Glover
- Department of Behavioral and Community Health, University of Maryland School of Public Health, College Park, MD, USA
| | - J Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - M D Shardell
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - C J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, USA.
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
| | - R M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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29
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Frikha Dammak D, Zarai Z, Najah S, Abdennabi R, Belbahri L, Rateb ME, Mejdoub H, Maalej S. Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1205258. [PMID: 28819625 PMCID: PMC5551467 DOI: 10.1155/2017/1205258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/18/2017] [Indexed: 02/07/2023]
Abstract
This study has focused on the isolation of twenty-three halophilic actinomycetes from two ponds of different salinity and the evaluation of their ability to exert an antimicrobial activity against both their competitors and several other pathogens. From the 23 isolates, 18 strains showed antagonistic activity, while 19 showed activities against one or more of the seven pathogen strains tested. Six strains exhibited consistent antibacterial activity against Gram-negative and Gram-positive pathogens characterized at the physiological and molecular levels. These strains shared only 94-95% 16S rRNA sequence identity with the closely related species of the Thermoactinomycetaceae family. Among them, the potent strain SMBg3 was further characterized and assigned to a new genus in the family for which the name Paludifilum halophilum (DSM 102817T) is proposed. Sequential extraction of the antimicrobial compounds with ethyl acetate revealed that the crude extract from SMBg3 strain had inhibitory effect on the growth of the plant pathogen Agrobacterium tumefaciens and the human pathogens Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa. Based on the HRESI-MS spectral data, the cyclic lipopeptide Gramicidin S and four cyclic dipeptides (CDPs) named cyclo(L-4-OH-Pro-L-Leu), cyclo(L-Tyr-L-Pro), cyclo(L-Phe-L-Pro), and cyclo(L-Leu-L-Pro) were detected in the fermentation broth of Paludifilum halophilum. To our knowledge, this is the first report on the isolation of these compounds from members of the Thermoactinomycetaceae family.
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Affiliation(s)
- Donyez Frikha Dammak
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Ziad Zarai
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS, BPW, 1173 Sfax, Tunisia
| | - Soumaya Najah
- Institut de Biologie Integrative, UMR 9198, Université Paris-Sud, Bat 400, 91405 Orsay Cedex, France
| | - Rayed Abdennabi
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Mostafa E. Rateb
- School of Science & Sport, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Hafedh Mejdoub
- Laboratoire des Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, FSS, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Sami Maalej
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
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30
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Jamal Q, Cho JY, Moon JH, Kim KY. Purification and antifungal characterization of Cyclo (D-Pro-L- Val) from Bacillus amyloliquefaciens Y1 against Fusarium graminearum to control head blight in wheat. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Borthwick AD, Da Costa NC. 2,5-diketopiperazines in food and beverages: Taste and bioactivity. Crit Rev Food Sci Nutr 2017; 57:718-742. [PMID: 25629623 DOI: 10.1080/10408398.2014.911142] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
2,5-Diketopiperazines (2,5-DKPs) have been found to occur in a wide range of food and beverages, and display an array of chemesthetic effects (bitter, astringent, metallic, and umami) that can contribute to the taste of a variety of foods. These smallest cyclic peptides also occur as natural products and have been found to display a variety of bioactivities from antibacterial, antifungal, to anthroprotective effects and have the potential to be used in the development of new functional foods. An overview of the synthesis of these small chiral molecules and their molecular properties is presented. The occurrence, taste, and bioactivity of all simple naturally occurring 2,5-DKPs to date have been reviewed and those found in food from yeasts, fungi, and bacteria that have been used in food preparation or contamination, as well as metabolites of sweeteners and antibiotics added to food are also reviewed.
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Affiliation(s)
| | - Neil C Da Costa
- b International Flavors & Fragrances, Inc. , Union Beach , New Jersey , USA
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Mangamuri UK, Muvva V, Poda S, Chitturi B, Yenamandra V. Bioactive natural products from Pseudonocardia endophytica VUK-10. J Genet Eng Biotechnol 2016; 14:261-267. [PMID: 30647624 PMCID: PMC6299850 DOI: 10.1016/j.jgeb.2016.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/19/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023]
Abstract
Two proline containing cyclic dipeptides (CDPs), cyclo (L-Pro-L-Tyr) (1) and cyclo (L-Pro-L-Phe) (2) were isolated from the fermentation broth of Pseudonocardia endophytica VUK-10 originating from the Nizampatnam mangrove ecosystem on the south coast of Andhra Pradesh, India. The structures of the compounds were established by 1H NMR and 13C NMR spectroscopy, FTIR and EIMS. The antimicrobial and cytotoxic activities of the compounds were tested against a variety of medicinally and agriculturally important bacteria and fungi as well as on the MDA-MB-231, OAW-42, HeLa and MCF-7 human cell lines. Xanthomonas malvacearum was most sensitive toward 1 (MIC 4 μg/ml), whereas compound 2 had good antibacterial activity against Xanthomonas campestris (MIC 8 μg/ml). Fusarium solani was highly sensitive toward 1 (MIC 16 μg/ml). The compounds were cytotoxic against the human cell lines at micro molar concentrations; the highest activity (IC50 < 10 μM) of 1 was recorded against the MDA-MB-231 cancer cell line.
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Affiliation(s)
- Usha Kiranmayi Mangamuri
- Department of Botany and Microbiology, Acharya Nagarjuna University, Guntur 522510, Andhra Pradesh, India
| | - Vijayalakshmi Muvva
- Department of Botany and Microbiology, Acharya Nagarjuna University, Guntur 522510, Andhra Pradesh, India
| | - Sudhakar Poda
- Department of Biotechnology, Acharya Nagarjuna University, Guntur 522510, Andhra Pradesh, India
| | - Bhujangarao Chitturi
- Organic Chemistry Division-I, Indian Institute of Chemical Technology, Hyderabad 500007, India
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33
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Synthesis and activity evaluation of the cyclic dipeptides arylidene N -alkoxydiketopiperazines. Bioorg Med Chem 2016; 24:5197-5205. [DOI: 10.1016/j.bmc.2016.08.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 11/17/2022]
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34
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Niu XD, Lv Z, Zhou XR, Wang HS. Insight into the key active sites of afChiA1 based on molecular dynamics simulations and free energy calculations. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1148265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Xiao D. Niu
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
| | - Zhuo Lv
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
| | - Xin R. Zhou
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
| | - Hong S. Wang
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
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Ravindranath PA, Sanner MF. AutoSite: an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms. Bioinformatics 2016; 32:3142-3149. [PMID: 27354702 DOI: 10.1093/bioinformatics/btw367] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. RESULTS We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. AVAILABILITY AND IMPLEMENTATION http://adfr.scripps.edu/AutoDockFR/autosite.html CONTACT: sanner@scripps.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pradeep Anand Ravindranath
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michel F Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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36
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Diketopiperazines derivatives isolated from Bacillus thuringiensis and Bacillus endophyticus , establishment of their configuration by X-ray and their synthesis. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.04.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Driowya M, Saber A, Marzag H, Demange L, Benhida R, Bougrin K. Microwave-Assisted Synthesis of Bioactive Six-Membered Heterocycles and Their Fused Analogues. Molecules 2016; 21:492. [PMID: 27089315 PMCID: PMC6273482 DOI: 10.3390/molecules21040492] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
This review describes the formation of six-membered heterocyclic compounds and their fused analogues under microwave activation using modern organic transformations including cyclocondensation, cycloaddition, multicomponents and other modular reactions. The review is divided according to the main heterocycle types in order of increasing complexity, starting with heterocyclic systems containing one, two and three heteroatoms and their fused analogues. Recent microwave applications are reviewed, with special focus on the chemistry of bioactive compounds. Selected examples from the 2006 to 2015 literature are discussed.
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Affiliation(s)
- Mohsine Driowya
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique, URAC23, Faculté des Sciences, Université Mohammed V, B.P. 1014 Rabat, Maroc.
| | - Aziza Saber
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique, URAC23, Faculté des Sciences, Université Mohammed V, B.P. 1014 Rabat, Maroc.
| | - Hamid Marzag
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique, URAC23, Faculté des Sciences, Université Mohammed V, B.P. 1014 Rabat, Maroc.
| | - Luc Demange
- Institut de Chimie de Nice, ICN UMR UNS CNRS 7272, Université Nice-Sophia Antipolis-Université Côte d'Azur, Parc Valrose, 06108 Nice Cedex 2, France.
- Department of Chemistry, Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Pharmaceutiques, 4 avenue de l'Observatoire & UFR Biomédicale des Saints Pères, 45 rue des Saints Pères, Paris Fr-75006, France.
| | - Rachid Benhida
- Institut de Chimie de Nice, ICN UMR UNS CNRS 7272, Université Nice-Sophia Antipolis-Université Côte d'Azur, Parc Valrose, 06108 Nice Cedex 2, France.
| | - Khalid Bougrin
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique, URAC23, Faculté des Sciences, Université Mohammed V, B.P. 1014 Rabat, Maroc.
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38
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Anticancer potential of pyrrole (1, 2, a) pyrazine 1, 4, dione, hexahydro 3-(2-methyl propyl) (PPDHMP) extracted from a new marine bacterium, Staphylococcus sp. strain MB30. Apoptosis 2016; 21:566-77. [DOI: 10.1007/s10495-016-1221-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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Li Y, Li F, Zhu Y, Li X, Zhou Z, Liu C, Zhang W, Tang M. DFT study on reaction mechanisms of cyclic dipeptide generation. Struct Chem 2016. [DOI: 10.1007/s11224-016-0740-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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40
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Hayasaka F, Yamamoto S, Sakai Y. Production Method for Cyclic Dipeptide Derived from Native Collagen. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2016. [DOI: 10.3136/fstr.22.477] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | | | - Yasuo Sakai
- Central Research Institute, Jellice Co., Ltd
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41
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Deepa I, Kumar SN, Sreerag RS, Nath VS, Mohandas C. Purification and synergistic antibacterial activity of arginine derived cyclic dipeptides, from Achromobacter sp. associated with a rhabditid entomopathogenic nematode against major clinically relevant biofilm forming wound bacteria. Front Microbiol 2015; 6:876. [PMID: 26379651 PMCID: PMC4548193 DOI: 10.3389/fmicb.2015.00876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/10/2015] [Indexed: 01/01/2023] Open
Abstract
Skin and chronic wound infections caused by various pathogenic bacteria are an increasing and urgent health problem worldwide. In the present investigation ethyl acetate extract of an Achromobacter sp. associated with a Rhabditis entomopathogenic nematode (EPN), displayed promising antibacterial property and was further purified by silica gel column chromatography to get three different cyclic dipeptides (CDPs). Based on the spectral data and Marfey's analyses, the CDPs were identified as cyclo(D-Leu-D-Arg) (1), cyclo(L-Trp-L-Arg) (2), and cyclo(D-Trp-D-Arg) (3), respectively. Three CDPs were active against all the 10 wound associated bacteria tested. The significant antibacterial activity was recorded by CDP 3, and highest activity of 0.5 μg/ml was recorded against Staphylococcus aureus and Pseudomonas aeruginosa. The synergistic antibacterial activities of CDPs and ampicillin were assessed using the checkerboard microdilution method. The results of the current study recorded that the combined effects of CDPs and ampicillin principally recorded synergistic activity. Interestingly, the combination of CDPs and ampicillin also recorded enhanced inhibition of biofilm formation by bacteria. Moreover, CDPs significantly stimulate the production of IL-10 and IL-4 (anti-inflammatory cytokines) by human peripheral blood mononuclear cells. CDPs do not make any significant effect on the production of pro-inflammatory cytokines like TNF-α. The three CDPs have been studied for their effect on intracellular S. aureus in murine macrophages (J774) using 24 h exposure to 0.5X, 1X, and 2X MIC concentrations. Significant decrease in intracellular S. aureus burden was recorded by CDPs. CDPs also recorded no cytotoxicity toward FS normal fibroblast, VERO, and L231 normal lung epithelial cell lines. Antimicrobial activity of the arginine containing CDPs against the wound associated bacteria is reported here for the first. Moreover, this is also the first report on the production of CDPs by Achromobacter sp. Finally, we conclude that the Achromobacter sp. is an incredibly promising source of natural bioactive secondary metabolites especially against wound pathogenic bacteria that may receive significant benefit in the field of human medicine in near future as topical agents.
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Affiliation(s)
- Indira Deepa
- Division of Crop Protection, Central Tuber Crops Research Institute Thiruvananthapuram, India
| | - Sasidharan N Kumar
- Division of Crop Protection, Central Tuber Crops Research Institute Thiruvananthapuram, India
| | - Ravikumar S Sreerag
- Division of Crop Protection, Central Tuber Crops Research Institute Thiruvananthapuram, India
| | - Vishnu S Nath
- Division of Crop Protection, Central Tuber Crops Research Institute Thiruvananthapuram, India
| | - Chellapan Mohandas
- Division of Crop Protection, Central Tuber Crops Research Institute Thiruvananthapuram, India
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42
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Jitonnom J, Sattayanon C, Kungwan N, Hannongbua S. A DFT study of the unusual substrate-assisted mechanism of Serratia marcescens chitinase B reveals the role of solvent and mutational effect on catalysis. J Mol Graph Model 2015; 56:53-9. [DOI: 10.1016/j.jmgm.2014.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
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43
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Kumar SN, Nambisan B. Antifungal activity of diketopiperazines and stilbenes against plant pathogenic fungi in vitro. Appl Biochem Biotechnol 2014; 172:741-54. [PMID: 24122628 DOI: 10.1007/s12010-013-0567-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Abstract
The present study aimed to investigate antifungal activity of a stilbene and diketopiperazine compounds against plant pathogenic fungi, including Phytophthora capsici, P. colocasiae, Botrytis cinerea and Colletotrichum gloeosporioides. Minimal inhibition concentrations (MIC) and minimal fungicidal concentrations (MFC) of stilbenes and diketopiperazines for each fungus were determined using microplate method. Best activity was recorded by stilbenes against P. capsici and P. colocasiae. All four test compounds were effective in inhibiting different stages of the life cycle of test fungi. Stilbenes were more effective than diketopiperazines in inhibiting mycelial growth and inhibiting different stages of the life cycle of P. capsici and P. colocasiae. Rupture of released zoospores induced by stilbenes was reduced by addition of 100 mM glucose. The effects of stilbenes on mycelial growth and zoospore release, but not zoospore rupture, were reduced largely when pH value was above 7. In addition, stilbenes were investigated for its antifungal stability against Phytophthora sp. The results showed that stilbenes maintained strong fungistatic activity over a wide pH range (pH 4–9) and temperature range (70–120 °C). The compound stilbenes exhibited strong and stable broad-spectrum antifungal activity, and had a significant fungicidal effect on fungal cells. Results from prebiocontrol evaluations performed to date are probably useful in the search for alternative approaches to controlling serious plant pathogens.
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Pereira PC, Arends IW, Sheldon RA. A green and expedient synthesis of enantiopure diketopiperazines via enzymatic resolution of unnatural amino acids. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.06.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Hong YP, Lee SH, Choi JH, Kashima A, Nakamura G, Suzuki T. Crystal Structure and Spectroscopic Properties of Cyclic Dipeptide: A Racemic Mixture of cyclo(ᴅ-Prolyl-ʟ-Tyrosyl) and cyclo(ʟ-Prolyl-ᴅ-Tyrosyl). B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.8.2299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Chen L, Zhou Y, Qu M, Zhao Y, Yang Q. Fully deacetylated chitooligosaccharides act as efficient glycoside hydrolase family 18 chitinase inhibitors. J Biol Chem 2014; 289:17932-40. [PMID: 24828498 DOI: 10.1074/jbc.m114.564534] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small molecule inhibitors against chitinases have potential applications as pesticides, fungicides, and antiasthmatics. Here, we report that a series of fully deacetylated chitooligosaccharides (GlcN)2-7 can act as inhibitors against the insect chitinase OfChtI, the human chitinase HsCht, and the bacterial chitinases SmChiA and SmChiB with IC50 values at micromolar to millimolar levels. The injection of mixed (GlcN)2-7 into the fifth instar larvae of the insect Ostrinia furnacalis resulted in 85% of the larvae being arrested at the larval stage and death after 10 days, also suggesting that (GlcN)2-7 might inhibit OfChtI in vivo. Crystal structures of the catalytic domain of OfChtI (OfChtI-CAD) complexed with (GlcN)5,6 were obtained at resolutions of 2.0 Å. These structures, together with mutagenesis and thermodynamic analysis, suggested that the inhibition was strongly related to the interaction between the -1 GlcN residue of the inhibitor and the catalytic Glu(148) of the enzyme. Structure-based comparison showed that the fully deacetylated chitooligosaccharides mimic the substrate chitooligosaccharides by binding to the active cleft. This work first reports the inhibitory activity and proposed inhibitory mechanism of fully deacetylated chitooligosaccharides. Because the fully deacetylated chitooligosaccharides can be easily derived from chitin, one of the most abundant materials in nature, this work also provides a platform for developing eco-friendly inhibitors against chitinases.
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Affiliation(s)
- Lei Chen
- From the School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, China
| | - Yong Zhou
- the School of Software, Dalian University of Technology, Dalian 116620, China, and
| | - Mingbo Qu
- From the School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, China
| | - Yong Zhao
- the Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qing Yang
- From the School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, China,
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Jitonnom J, Limb MAL, Mulholland AJ. QM/MM free-energy simulations of reaction in Serratia marcescens Chitinase B reveal the protonation state of Asp142 and the critical role of Tyr214. J Phys Chem B 2014; 118:4771-83. [PMID: 24730355 DOI: 10.1021/jp500652x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Serratia marcescens Chitinase B (ChiB), belonging to the glycosidase family 18 (GH18), catalyzes the hydrolysis of β-1,4-glycosidic bond, with retention of configuration, via an unusual substrate-assisted mechanism, in which the substrate itself acts as an intramolecular nucleophile. Here, both elementary steps (glycosylation and deglycosylation) of the ChiB-catalyzed reaction are investigated by means of combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations at the SCC-DFTB/CHARMM22 level of theory. We examine the influence of the Asp142 protonation state on the reaction and the role that this residue performs in the reaction. Our simulations show that reaction with a neutral Asp142 is preferred and demonstrate that this residue provides electrostatic stabilization of the oxazolinium ion intermediate formed in the reaction. Insight into the conformational itinerary ((1,4)B↔(4)H5↔(4)C1) adopted by the substrate (bound in subsite -1) along the preferred reaction pathway is also provided by the simulations. The relative energies of the stationary points found along the reaction pathway calculated with SCC-DFTB and B3LYP were compared. The results suggest that SCC-DFTB is an accurate method for estimating the relative barriers for both steps of the reaction; however, it was found to overestimate the relative energy of an intermediate formed in the reaction when compared with the higher level of theory. Glycosylation is suggested to be a rate-determining step in the reaction with calculated overall reaction free-energy barrier of 20.5 kcal/mol, in a reasonable agreement with the 16.1 kcal/mol barrier derived from the experiment. The role of Tyr214 in catalysis was also investigated with the results, indicating that the residue plays a critical role in the deglycosylation step of the reaction. Simulations of the enzyme-product complex were also performed with an unbinding event suggested to have been observed, affording potential new mechanistic insight into the release of the product of ChiB.
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Affiliation(s)
- Jitrayut Jitonnom
- Division of Chemistry, School of Science, University of Phayao , Phayao 56000, Thailand
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48
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Efficient synthesis of heterocyclic compounds derived from 2,6-dioxopiperazine derivatives and their evaluation for anti-inflammatory and anticancer activities. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0969-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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49
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Koopmanschap G, Ruijter E, Orru RVA. Isocyanide-based multicomponent reactions towards cyclic constrained peptidomimetics. Beilstein J Org Chem 2014; 10:544-98. [PMID: 24605172 PMCID: PMC3943360 DOI: 10.3762/bjoc.10.50] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/24/2014] [Indexed: 12/16/2022] Open
Abstract
In the recent past, the design and synthesis of peptide mimics (peptidomimetics) has received much attention. This because they have shown in many cases enhanced pharmacological properties over their natural peptide analogues. In particular, the incorporation of cyclic constructs into peptides is of high interest as they reduce the flexibility of the peptide enhancing often affinity for a certain receptor. Moreover, these cyclic mimics force the molecule into a well-defined secondary structure. Constraint structural and conformational features are often found in biological active peptides. For the synthesis of cyclic constrained peptidomimetics usually a sequence of multiple reactions has been applied, which makes it difficult to easily introduce structural diversity necessary for fine tuning the biological activity. A promising approach to tackle this problem is the use of multicomponent reactions (MCRs), because they can introduce both structural diversity and molecular complexity in only one step. Among the MCRs, the isocyanide-based multicomponent reactions (IMCRs) are most relevant for the synthesis of peptidomimetics because they provide peptide-like products. However, these IMCRs usually give linear products and in order to obtain cyclic constrained peptidomimetics, the acyclic products have to be cyclized via additional cyclization strategies. This is possible via incorporation of bifunctional substrates into the initial IMCR. Examples of such bifunctional groups are N-protected amino acids, convertible isocyanides or MCR-components that bear an additional alkene, alkyne or azide moiety and can be cyclized via either a deprotection-cyclization strategy, a ring-closing metathesis, a 1,3-dipolar cycloaddition or even via a sequence of multiple multicomponent reactions. The sequential IMCR-cyclization reactions can afford small cyclic peptide mimics (ranging from four- to seven-membered rings), medium-sized cyclic constructs or peptidic macrocycles (>12 membered rings). This review describes the developments since 2002 of IMCRs-cyclization strategies towards a wide variety of small cyclic mimics, medium sized cyclic constructs and macrocyclic peptidomimetics.
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Affiliation(s)
- Gijs Koopmanschap
- Department of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Eelco Ruijter
- Department of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Romano VA Orru
- Department of Chemistry & Pharmaceutical Sciences, Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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50
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Sun X, Rai R, MacKerell AD, Faden AI, Xue F. Facile one-step synthesis of 2,5-diketopiperazines. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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