1
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Hu L, Lin J, Qin F, Xu L, Luo L. Exploring Sources, Biological Functions, and Potential Applications of the Ubiquitous Marine Cyclic Dipeptide: A Concise Review of Cyclic Glycine-Proline. Mar Drugs 2024; 22:271. [PMID: 38921582 PMCID: PMC11205142 DOI: 10.3390/md22060271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Cyclic glycine-proline (cGP), a prevalent marine cyclic dipeptide, possesses a distinct pyrrolidine-2,5-dione scaffold, which contributes to the chemical diversity and broad bioactivities of cGP. The diverse sources from marine-related, endogenous biological, and synthetic pathways and the in vitro and in vivo activities of cGP are reviewed. The potential applications for cGP are also explored. In particular, the pivotal roles of cGP in regulating insulin-like growth factor-1 homeostasis, enhancing neuroprotective effects, and improving neurotrophic function in central nervous system diseases are described. The potential roles of this endogenous cyclic peptide in drug development and healthcare initiatives are also highlighted. This review underscores the significance of cGP as a fundamental building block in drug discovery with exceptional drug-like properties and safety. By elucidating the considerable value of cGP, this review aims to reignite interest in cGP-related research within marine medicinal chemistry and synthetic biology.
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Affiliation(s)
- Lei Hu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Jing Lin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Fei Qin
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Li Xu
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
| | - Lianzhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361023, China; (J.L.); (F.Q.); (L.X.)
- Fujian Province University Marine Biopharmaceutical Resource Engineering Research Center, Xiamen Medical College, Xiamen 361023, China
- School of Pharmacy and Pharmaceutical Sciences, Xiamen Medical College, Xiamen 361023, China
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2
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da Silva Ripardo-Filho H, Coca Ruíz V, Suárez I, Moraga J, Aleu J, Collado IG. From Genes to Molecules, Secondary Metabolism in Botrytis cinerea: New Insights into Anamorphic and Teleomorphic Stages. PLANTS (BASEL, SWITZERLAND) 2023; 12:553. [PMID: 36771642 PMCID: PMC9920419 DOI: 10.3390/plants12030553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The ascomycete Botrytis cinerea Pers. Fr., classified within the family Sclerotiniaceae, is the agent that causes grey mould disease which infects at least 1400 plant species, including crops of economic importance such as grapes and strawberries. The life cycle of B. cinerea consists of two phases: asexual (anamorph, Botrytis cinerea Pers. Fr.) and sexual (teleomorph, Botryotinia fuckeliana (de Bary) Wetzel). During the XVI International Symposium dedicated to the Botrytis fungus, which was held in Bari in June 2013, the scientific community unanimously decided to assign the most widely used name of the asexual form, Botrytis, to this genus of fungi. However, in the literature, we continue to find articles referring to both morphic stages. In this review, we take stock of the genes and metabolites reported for both morphic forms of B. cinerea between January 2015 and October 2022.
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Affiliation(s)
| | - Víctor Coca Ruíz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Ivonne Suárez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Javier Moraga
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
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3
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Guo X, Fu S, Ying J, Zhao Y. Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization. Open Biol 2023; 13:220234. [PMID: 36629018 PMCID: PMC9832566 DOI: 10.1098/rsob.220234] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent.
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Affiliation(s)
- Xiaofan Guo
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Songsen Fu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China,Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, People's Republic of China
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4
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Boigenzahn H, Yin J. Glycine to Oligoglycine via Sequential Trimetaphosphate Activation Steps in Drying Environments. ORIGINS LIFE EVOL B 2022; 52:249-261. [DOI: 10.1007/s11084-022-09634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022]
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5
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Gan D, Ying J, Zhao Y. Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution. Front Chem 2022; 10:941228. [PMID: 35910738 PMCID: PMC9326000 DOI: 10.3389/fchem.2022.941228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 11/22/2022] Open
Abstract
Life’s origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth’s biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the “mystery of life".
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Affiliation(s)
- Dingwei Gan
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- *Correspondence: Jianxi Ying,
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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6
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Carlini L, Chiarinelli J, Mattioli G, Castrovilli MC, Valentini V, De Stefanis A, Bauer EM, Bolognesi P, Avaldi L. Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide. J Phys Chem B 2022; 126:2968-2978. [PMID: 35438499 PMCID: PMC9059117 DOI: 10.1021/acs.jpcb.1c10736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Dipeptides, the prototype
peptides, exist in both linear (l-) and cyclo (c-) structures. Since the
first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a
temperature-induced process. In this work, combining several different
experimental techniques (mass spectrometry, infrared and Raman spectroscopy,
and thermogravimetric analysis) with tight-binding and ab initio simulations,
we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed
by water and driven by temperature, occurs in the condensed phase.
This process can be considered as a very efficient strategy to improve
dipeptide stability by turning the comparatively fragile linear structure
into the robust and more stable cyclic one. This mechanism may have
played a role in prebiotic chemistry and can be further exploited
in the preparation of nanomaterials and drugs.
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Affiliation(s)
- Laura Carlini
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Giuseppe Mattioli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Mattea Carmen Castrovilli
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Veronica Valentini
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Adriana De Stefanis
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Elvira Maria Bauer
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo 00015, Italy
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7
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Chiarinelli J, Barreiro-Lage D, Bolognesi P, RICHTER R, Zettergren H, Stockett MH, Díaz-Tendero S, Avaldi L. Electron and ion spectroscopy of the cyclo-alanine-alanine dipeptide. Phys Chem Chem Phys 2022; 24:5855-5867. [DOI: 10.1039/d1cp05811h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The VUV photoionisation and photofragmentation of cyclo-alanine-alanine (cAA) has been studiedin a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron-photoion coincidence (PEPICO) measurements, which enable a control...
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8
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Molteni E, Mattioli G, Alippi P, Avaldi L, Bolognesi P, Carlini L, Vismarra F, Wu Y, Varillas RB, Nisoli M, Singh M, Valadan M, Altucci C, Richter R, Sangalli D. A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase. Phys Chem Chem Phys 2021; 23:26793-26805. [PMID: 34816853 DOI: 10.1039/d1cp04050b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.
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Affiliation(s)
- Elena Molteni
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
| | - Giuseppe Mattioli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Alippi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Bolognesi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Laura Carlini
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Federico Vismarra
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Yingxuan Wu
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | | | - Mauro Nisoli
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Manjot Singh
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy
| | - Mohammadhassan Valadan
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Robert Richter
- Sincrotrone Trieste, Area Science Park, Basovizza, Trieste, Italy
| | - Davide Sangalli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
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9
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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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10
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Ying J, Ding R, Liu Y, Zhao Y. Prebiotic Chemistry in Aqueous Environment: A Review of Peptide Synthesis and Its Relationship with Genetic Code. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianxi Ying
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Yan Liu
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
| | - Yufen Zhao
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
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11
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Guo Y, Ying J, Sun D, Zhang Y, Zheng M, Ding R, Liu Y, Zhao Y. Cyclic Dipeptides Formation From Linear Dipeptides Under Potentially Prebiotic Earth Conditions. Front Chem 2021; 9:675821. [PMID: 34262893 PMCID: PMC8273163 DOI: 10.3389/fchem.2021.675821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/14/2021] [Indexed: 11/30/2022] Open
Abstract
Cyclic dipeptides (DKPs) are peptide precursors and chiral catalysts in the prebiotic process. This study reports proline-containing DKPs that were spontaneously obtained from linear dipeptides under an aqueous solution. Significantly, the yields of DKPs were affected by the sequence of linear dipeptides and whether the reaction contains trimetaphosphate. These findings provide the possibility that DKPs might play a key role in the origin of life.
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Affiliation(s)
- Yeting Guo
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Yumeng Zhang
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Minyang Zheng
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Yan Liu
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China.,Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.,Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
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12
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Scarel M, Marchesan S. Diketopiperazine Gels: New Horizons from the Self-Assembly of Cyclic Dipeptides. Molecules 2021; 26:3376. [PMID: 34204905 PMCID: PMC8199760 DOI: 10.3390/molecules26113376] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cyclodipeptides (CDPs) or 2,5-diketopiperazines (DKPs) can exert a variety of biological activities and display pronounced resistance against enzymatic hydrolysis as well as a propensity towards self-assembly into gels, relative to the linear-dipeptide counterparts. They have attracted great interest in a variety of fields spanning from functional materials to drug discovery. This concise review will analyze the latest advancements in their synthesis, self-assembly into gels, and their more innovative applications.
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Affiliation(s)
- Marco Scarel
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
- National Interuniversity Consortium of Materials Science and Technology (INSTM), University of Trieste, 34127 Trieste, Italy
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13
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Apostolopoulos V, Bojarska J, Chai TT, Elnagdy S, Kaczmarek K, Matsoukas J, New R, Parang K, Lopez OP, Parhiz H, Perera CO, Pickholz M, Remko M, Saviano M, Skwarczynski M, Tang Y, Wolf WM, Yoshiya T, Zabrocki J, Zielenkiewicz P, AlKhazindar M, Barriga V, Kelaidonis K, Sarasia EM, Toth I. A Global Review on Short Peptides: Frontiers and Perspectives. Molecules 2021; 26:E430. [PMID: 33467522 PMCID: PMC7830668 DOI: 10.3390/molecules26020430] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide "drugs" initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.
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Affiliation(s)
- Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (V.A.); (J.M.); (V.B.)
| | - Joanna Bojarska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Tsun-Thai Chai
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia;
| | - Sherif Elnagdy
- Botany and Microbiology Department, Faculty of Science, Cairo University, Gamaa St., Giza 12613, Egypt; (S.E.); (M.A.)
| | - Krzysztof Kaczmarek
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (K.K.); (J.Z.)
| | - John Matsoukas
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (V.A.); (J.M.); (V.B.)
- NewDrug, Patras Science Park, 26500 Patras, Greece;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Roger New
- Vaxcine (UK) Ltd., c/o London Bioscience Innovation Centre, London NW1 0NH, UK;
- Faculty of Science & Technology, Middlesex University, The Burroughs, London NW4 4BT, UK;
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA;
| | - Octavio Paredes Lopez
- Centro de Investigación y de Estudios Avanzados del IPN, Departamento de Biotecnología y Bioquímica, Irapuato 36824, Guanajuato, Mexico;
| | - Hamideh Parhiz
- Infectious Disease Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6073, USA;
| | - Conrad O. Perera
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Monica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina;
- Instituto de Física de Buenos Aires (IFIBA, UBA-CONICET), Argentina, Buenos Aires 1428, Argentina
| | - Milan Remko
- Remedika, Luzna 9, 85104 Bratislava, Slovakia;
| | - Michele Saviano
- Institute of Crystallography (CNR), Via Amendola 122/o, 70126 Bari, Italy;
| | - Mariusz Skwarczynski
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (M.S.); (I.T.)
| | - Yefeng Tang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (MOE), School of Pharma Ceutical Sciences, Tsinghua University, Beijing 100084, China;
| | - Wojciech M. Wolf
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | | | - Janusz Zabrocki
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (K.K.); (J.Z.)
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
- Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Maha AlKhazindar
- Botany and Microbiology Department, Faculty of Science, Cairo University, Gamaa St., Giza 12613, Egypt; (S.E.); (M.A.)
| | - Vanessa Barriga
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (V.A.); (J.M.); (V.B.)
| | | | | | - Istvan Toth
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (M.S.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
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14
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Zhao Z, Cheng S, Mao Y, Ying J, Tian S, Zhao Y. Primary Research of the Relationship between Genetic Codons and Amino Acids Based on the Technology of Electronic Tongue. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a21070334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Petsi M, Zografos AL. 2,5-Diketopiperazine Catalysts as Activators of Dioxygen in Oxidative Processes. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01847] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Marina Petsi
- Department of Chemistry, Main University Campus, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Alexandros L. Zografos
- Department of Chemistry, Main University Campus, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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16
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Kleinsmann AJ, Nachtsheim BJ. A minimalistic hydrolase based on co-assembled cyclic dipeptides. Org Biomol Chem 2020; 18:102-107. [PMID: 31799587 DOI: 10.1039/c9ob02198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.
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Affiliation(s)
- Alexander J Kleinsmann
- Institut für Organische Chemie Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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17
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Procházková E, Filo J, Cigáň M, Baszczyňski O. Sterically-Controlled Self-Immolation in Phosphoramidate Linkers Triggered by Light. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eliška Procházková
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences, Flemingovo nám. 542/2; 116 10 Prague Czech Republic
| | - Juraj Filo
- Institute of Chemistry, Faculty of Natural Sciences; Comenius University, Ilkovičova 6; Bratislava 842 15 Slovakia
| | - Marek Cigáň
- Institute of Chemistry, Faculty of Natural Sciences; Comenius University, Ilkovičova 6; Bratislava 842 15 Slovakia
| | - Ondřej Baszczyňski
- Department of Organic Chemistry, Faculty of Science; Charles University, Hlavova 2030/8; 128 43 Prague Czech Republic
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18
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Maguire OR, Taylor B, Higgins EM, Rees M, Cobb SL, Simpkins NS, Hayes CJ, O'Donoghue AC. Unusually high α-proton acidity of prolyl residues in cyclic peptides. Chem Sci 2020; 11:7722-7729. [PMID: 34094148 PMCID: PMC8159430 DOI: 10.1039/d0sc02508a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The acidity of the α-proton in peptides has an essential role in numerous biochemical reactions and underpins their stereochemical integrity, which is critical to their biological function. We report a detailed kinetic and computational study of the acidity of the α-proton in two cyclic peptide systems: diketopiperazine (DKP) and triketopiperazine (TKP). The kinetic acidity (protofugality) of the α-protons were determined though hydrogen deuterium exchange studies in aqueous solutions. The acidities of the α-proton in prolyl residues were increased by 3–89 fold relative to other amino acid residues (prolyl > glycyl ≫ alanyl > tyrosyl). Experimental and computational evidence for the stereoelectronic origins of this enhanced prolyl reactivity is presented. TKPs were 106-fold more reactive than their DKP analogues towards deprotonation, which we attribute to the advanced development of aromaticity in the earlier transition state for proton transfer in these cases. A Brønsted linear free energy analysis of the reaction data was conducted to provide estimates of α-proton pKas. Kinetic and computational studies reveal that prolyl residues in cyclic peptides are substantially more acidic than other residues due to a stereoelectronic effect.![]()
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Affiliation(s)
| | - Bethany Taylor
- Department of Chemistry
- Durham University
- Durham DH1 3LE
- UK
| | | | - Matthew Rees
- School of Chemistry
- University of Birmingham
- Birmingham
- UK
| | - Steven L. Cobb
- Department of Chemistry
- Durham University
- Durham DH1 3LE
- UK
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19
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Ziganshin MA, Larionov RA, Gerasimov AV, Ziganshina SA, Klimovitskii AE, Khayarov KR, Mukhametzyanov TA, Gorbatchuk VV. Thermally induced cyclization of L -isoleucyl- L -alanine in solid state: Effect of dipeptide structure on reaction temperature and self-assembly. J Pept Sci 2019; 25:e3177. [PMID: 31317614 DOI: 10.1002/psc.3177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022]
Abstract
Thermal treatment of short-chain oligopeptides is able to initiate the process of their self-assembly with the formation of organic nanostructures with unique properties. On the other hand, heating can lead to a chemical reaction with the formation of new substances with specific properties and ability to form structures with different morphology. Therefore, in order to have a desired process, researcher needs to find its temperature range. In the present work, cyclization of L -isoleucyl-L -alanine dipeptide in the solid state upon heating was studied. Kinetic parameters of this reaction were estimated within the approaches of the nonisothermal kinetics. The correlation between side chain structure of dipeptides and temperature of their cyclization in the solid state was found for the first time. This correlation may be used to predict the temperature, at which dipeptide self-assembly changes to chemical reaction. The differences in self-assembly of linear and cyclic dipeptides were demonstrated using atomic force microscopy. The effect of dipeptide concentration in a source solution and an organic solvent used on self-assembly of dipeptides was shown. The new information obtained on the thermal properties and self-assembly of linear and cyclic forms of L -isoleucyl-L -alanine may be useful for the design of new nanomaterials based on oligopeptides, as well as for the synthesis of cyclic oligopeptides.
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Affiliation(s)
- Marat A Ziganshin
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | - Radik A Larionov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | | | - Sufia A Ziganshina
- Zavoisky Physical-Technical Institute of FRC Kazan Scientific Center of RAS, Kazan, Russia
| | | | - Khasan R Khayarov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | | | - Valery V Gorbatchuk
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
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20
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Affiliation(s)
- Matthew A. Pasek
- School of Geosciences, University of South Florida, 4202 E. Fowler Avenue NES 204, Tampa, Florida 33620, United States
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21
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Single-Frame, Multiple-Frame and Framing Motifs in Genes. Life (Basel) 2019; 9:life9010018. [PMID: 30744207 PMCID: PMC6463195 DOI: 10.3390/life9010018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022] Open
Abstract
We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is SF as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame SF is multiple-frame MF. Several classes of MF motifs are defined and analysed. The distributions of single-frame SF motifs (associated with an unambiguous trinucleotide decoding in the two 5′–3′ and 3′–5′ directions) and 5′ unambiguous motifs 5′U (associated with an unambiguous trinucleotide decoding in the 5′–3′ direction only) are analysed without and with constraints. The constraints studied are: initiation and stop codons, periodic codons {AAA,CCC,GGG,TTT}, antiparallel complementarity and parallel complementarity. Taken together, these results suggest that the complementarity property involved in the antiparallel (DNA double helix, RNA stem) and parallel sequences could also be fundamental for coding genes with an unambiguous trinucleotide decoding in the two 5′–3′ and 3′–5′ directions or the 5′–3′ direction only. Furthermore, the single-frame motifs SF with a property of trinucleotide decoding and the framing motifs F (also called circular code motifs; first introduced by Michel (2012)) with a property of reading frame decoding may have been involved in the early life genes to build the modern genetic code and the extant genes. They could have been involved in the stage without anticodon-amino acid interactions or in the Implicated Site Nucleotides (ISN) of RNA interacting with the amino acids. Finally, the SF and MF dipeptides associated with the SF and MF dicodons, respectively, are studied and their importance for biology and the origin of life discussed.
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22
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Sibilska I, Feng Y, Li L, Yin J. Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH. ORIGINS LIFE EVOL B 2018; 48:277-287. [PMID: 30269289 DOI: 10.1007/s11084-018-9564-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 09/16/2018] [Indexed: 11/26/2022]
Abstract
The biochemical activation of amino acids by adenosine triphosphate (ATP) drives the synthesis of proteins that are essential for all life. On the early Earth, before the emergence of cellular life, the chemical condensation of amino acids to form prebiotic peptides or proteins may have been activated by inorganic polyphosphates, such as tri metaphosphate (TP). Plausible volcanic and other potential sources of TP are known, and TP readily activates amino acids for peptide synthesis. But de novo peptide synthesis also depends on pH, temperature, and processes of solvent drying, which together define a varied range of potential activating conditions. Although we cannot replay the tape of life on Earth, we can examine how activator, temperature, acidity and other conditions may have collectively shaped its prebiotic evolution. Here, reactions of two simple amino acids, glycine and alanine, were tested, with or without TP, over a wide range of temperature (0-100 °C) and acidity (pH 1-12), while open to the atmosphere. After 24 h, products were analyzed by HPLC and mass spectrometry. In the absence of TP, glycine and alanine readily formed peptides under harsh near-boiling temperatures, extremes of pH, and within dry solid residues. In the presence of TP, however, peptides arose over a much wider range of conditions, including ambient temperature, neutral pH, and in water. These results show how polyphosphates such as TP may have enabled the transition of peptide synthesis from harsh to mild early Earth environments, setting the stage for the emergence of more complex prebiotic chemistries.
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Affiliation(s)
- Izabela Sibilska
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Yu Feng
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - John Yin
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA.
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA.
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23
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Mimura K, Okada R, Nishida T. Chiral gas chromatography of 2,5-diketopiperazines following a ring-opening derivatization method for complete isomeric separation. J Chromatogr A 2018; 1566:118-123. [DOI: 10.1016/j.chroma.2018.06.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/24/2022]
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24
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Ying J, Fu S, Li X, Feng L, Xu P, Liu Y, Gao X, Zhao Y. A plausible model correlates prebiotic peptide synthesis with the primordial genetic code. Chem Commun (Camb) 2018; 54:8598-8601. [PMID: 30014068 DOI: 10.1039/c8cc04767g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Aminoacyladenylates (5'-aa-AMPs) are key intermediates in peptide synthesis. Here we report analogs of 5'-aa-AMPs, namely nucleotide amidates (aa-N-NMPs), obtained under Hadean conditions. Significantly, dipeptides were detected from the above reactions and their yields varied with different nucleosides through the formation of different aa-N-NMPs. This model provides both prebiotic peptides and the primordial version of the genetic code through reactions that occurred under potentially prebiotic conditions.
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Affiliation(s)
- Jianxi Ying
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province and High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China. and Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Songsen Fu
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province and High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China.
| | - Xin Li
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province and High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China.
| | - Liubin Feng
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province and High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China.
| | - Pengxiang Xu
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province and High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China.
| | - Yan Liu
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province and High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China.
| | - Xiang Gao
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yufen Zhao
- Department of Chemical Biology, Key Laboratory for Chemical Biology of Fujian Province and High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China. and Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China and Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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