1
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Deck LT, Hosseinalipour MS, Mazzotti M. Spontaneous Emergence of Homochiral Suspensions from Racemic Solutions via Stochastic Nucleation. J Am Chem Soc 2025. [PMID: 40413642 DOI: 10.1021/jacs.5c02651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
Abstract
Homochirality represents a hallmark of life, and its emergence on the prebiotic Earth remains elusive. Here, we demonstrate a spontaneous pathway to homochirality, where a conglomerate-forming chiral species (N-(2-methylbenzylidene)-phenylglycine amide, NMPA) evolves from an initial perfectly symmetric state, i.e., a racemic solution, to a fully homochiral state, where only enantiopure crystals of one handedness are present in the suspension. It entails first the establishment of supersaturated conditions, e.g., because of either solvent evaporation or cooling, then stochastic nucleation of enantiopure crystals as the symmetry-breaking event, and finally asymmetry amplification and complete deracemization via temperature fluctuations in a racemizing solution (thanks to the presence of the base 1,8- diazabicyclo[5.4.0]undec-7-en, DBU). After developing a stochastic modeling platform and an experimental setup, we confirm the plausibility of this pathway through both detailed simulations and laboratory experiments. We also show how from a variety of local homochiral states of different handedness a global homochiral state may emerge via merging and deracemizing. Because the external conditions triggering supersaturation creation, nucleation, and deracemization via temperature-cycling must have existed also on the prebiotic Earth, the proposed spontaneous pathway may have plausibly played a role in the emergence of life on Earth.
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Affiliation(s)
- Leif-Thore Deck
- Institute of Energy and Process Engineering, ETH Zurich, Zurich 8092, Switzerland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | | | - Marco Mazzotti
- Institute of Energy and Process Engineering, ETH Zurich, Zurich 8092, Switzerland
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2
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Greenwood JB, Donnelly L. Quantum control of photoion circular dichroism using orthogonal laser beams. Phys Chem Chem Phys 2025. [PMID: 40365660 DOI: 10.1039/d5cp01127b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
The circular dichroism manifested in the photoionization yields of the chiral molecule fenchone has been investigated using two laser beams of different wavelengths intersecting at 90 degrees. This allowed different two-colour ionization schemes to be investigated so that the circular dichroism contributions of each step in the multiphoton ionization process could be deduced. The results showed that the circular dichroism generated by a beam at a wavelength of 260 nm could be strongly influenced by the polarization state of a 520 nm beam propagating in a perpendicular direction. The asymmetry in the ion yields was found to change depending on whether the 520 nm beam was left or right circularly polarized, and if it was linear polarized in a direction parallel or perpendicular to the propagation direction of the 260 nm beam. The control exhibited by the direction of the linearly polarized light is attributed to an orientation dependence of the circular dichroism due to selective excitation of the isotropic ensemble by the 520 nm beam. By contrast, when both beams were circularly polarized, the dependence on the polarization direction of the 520 nm pulse is ascribed to either the interference between different ionization pathways or excitation of a chiral vibronic wavepacket in the molecule. These results are the first demonstration of chiroptical quantum control of total ion yields, showing in principle that all-optical enantio-sensitive chemical processing may be possible in the future.
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Affiliation(s)
- Jason B Greenwood
- Centre for Light-Matter Interactions, School of Mathematics and Physics, Queen's University Belfast, Belfast, UK.
| | - Leah Donnelly
- Centre for Light-Matter Interactions, School of Mathematics and Physics, Queen's University Belfast, Belfast, UK.
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3
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Molland DP, Rhyu IB, Wade J, Schnell JR. Bivalent Surface Attachment via Cysteine Thiol Results in Efficient and Stereoselective Abiotic Peptide Synthesis. JACS AU 2025; 5:1922-1931. [PMID: 40313818 PMCID: PMC12041950 DOI: 10.1021/jacsau.5c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 05/03/2025]
Abstract
Surface-catalyzed peptide bond formation may have been an important source of peptides for abiogenesis, but model peptide synthesis reactions using the consensus set of 10 abiotic amino acids give only modest rates of peptide bond formation. Additionally, the peptides are typically limited in length to a small number of amino acids and stereoselective amino acid incorporation is weak or absent. An abiotic route for the high-yield synthesis of cysteine from serine was recently reported by Foden et al. (Science 2020, 370, 865-869), indicating that, in some environments, prebiotic cysteine may also have been available. Here, we show that the presence of cysteine dramatically increases the yields of surface-catalyzed peptide synthesis reactions in a hydrothermal vent solvent model containing achiral silicate minerals and that the reaction exhibits a strong stereoselective bias toward l-cysteine. Solid state NMR confirmed that cysteine associates bivalently with silicates at alkaline pH via both the carboxylate and the sulfur groups. Polarization-resolved IRRAS indicates that the bivalent adsorption stereospecifically orients the reactive amino group, providing a mechanism for stereoselective incorporation of l-cysteine. Stereoselective rates of peptide bond formation in surface-catalyzed peptide bond formation are expected to occur for any amino acid able to form sufficiently strong side chain-silicate interactions at alkaline pH. The high nucleophilicity of the thiol group produces unusually high reaction rates and stereoselectivity in such reactions, in addition to conferring transition metal ion binding to the peptide products. The potential benefits of reactive sulfur species for abiogenesis suggest that they may be useful biosignatures in the search for habitable extraterrestrial environments.
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Affiliation(s)
- Daniel P. Molland
- Department
of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, U.K.
| | - Isabella B. Rhyu
- Department
of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, U.K.
| | - Jon Wade
- Department
of Earth Sciences, University of Oxford, South Parks Road, OX1 3AN Oxford, U.K.
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, U.K.
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4
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Okita H, Murayama K, Asanuma H. Chirality-Promoted Chemical Ligation and Reverse Transcription of Acyclic Threoninol Nucleic Acid. J Am Chem Soc 2025. [PMID: 40245353 DOI: 10.1021/jacs.5c03128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2025]
Abstract
The building blocks of current life on Earth are chiral compounds, such as 2'-deoxy-D-ribose of DNA and L-amino acids with homochirality, which play an important role in various biological reactions. We investigated the effect of chirality on the template-directed chemical synthesis of nucleic acids as a model for primitive replication of genetic materials in the absence of enzymes. The efficiency of the template-directed chemical ligation of two acyclic nucleic acids, achiral serinol nucleic acid (SNA) and chiral acyclic l-threoninol nucleic acid (L-aTNA), induced by N-cyanoimidazole and a divalent metal cation, was evaluated. The chemical ligation of SNA fragments on an SNA template was much slower than the ligation of L-aTNA fragments on an L-aTNA template. Examination of L-aTNA and SNA heteroligation and the effects of chimeric template strands revealed the crucial importance of L-aTNA chirality, which induces helical propagation and fixes the local conformation of the reactive phosphate group for effective chemical ligation. DNA and RNA templates also enhanced the ligation of SNA and L-aTNA fragments. "Reverse transcription" from template RNA to L-aTNA was also demonstrated. Our findings show that scaffold chirality is crucial for chemical replication and reverse transcription in XNA-based systems. Furthermore, the reverse transcription from RNA to L-aTNA will find applications in XNA-based in vitro selection, the creation of artificial life, and nanotechnologies.
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Affiliation(s)
- Hikari Okita
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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5
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Parker MC, Jeynes C, Walker SD. A Metric for the Entropic Purpose of a System. ENTROPY (BASEL, SWITZERLAND) 2025; 27:131. [PMID: 40003129 PMCID: PMC11854410 DOI: 10.3390/e27020131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/18/2025] [Accepted: 01/20/2025] [Indexed: 02/27/2025]
Abstract
Purpose in systems is considered to be beyond the purview of science since it is thought to be intrinsically personal. However, just as Claude Shannon was able to define an impersonal measure of information, so we formally define the (impersonal) 'entropic purpose' of an information system (using the theoretical apparatus of Quantitative Geometrical Thermodynamics) as the line integral of an entropic "purposive" Lagrangian defined in hyperbolic space across the complex temporal plane. We verify that this Lagrangian is well-formed: it has the appropriate variational (Euler-Lagrange) behaviour. We also discuss the teleological characteristics of such variational behaviour (featuring both thermodynamically reversible and irreversible temporal measures), so that a "Principle of Least (entropic) Purpose" can be adduced for any information-producing system. We show that entropic purpose is (approximately) identified with the information created by the system: an empirically measurable quantity. Exploiting the relationship between the entropy production of a system and its energy Hamiltonian, we also show how Landauer's principle also applies to the creation of information; any purposive system that creates information will also dissipate energy. Finally, we discuss how 'entropic purpose' might be applied in artificial intelligence contexts (where degrees of system 'aliveness' need to be assessed), and in cybersecurity (where this metric for 'entropic purpose' might be exploited to help distinguish between people and bots).
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Affiliation(s)
- Michael C. Parker
- School of Computer Science and Electrical Engineering, University of Essex, Colchester CO4 3SQ, UK
| | | | - Stuart D. Walker
- School of Computer Science and Electrical Engineering, University of Essex, Colchester CO4 3SQ, UK
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6
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Yao L, Pan C, Li W, Zhang J, Zhang Y, Jin T, Wang G, Sheng P, Zhang J, Yin X. Seeding Control in Chirality Triggering of Red-Emitting Organic Charge-Transfer Cocrystal Helixes from Achiral Molecules. ACS APPLIED MATERIALS & INTERFACES 2025; 17:1953-1961. [PMID: 39702952 DOI: 10.1021/acsami.4c17087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Supramolecular chirality has gained immense attention for great potential, in which the rational engineering strategy facilitates unique helical stacking/assembly, high chiroptical behavior, and prime biomedical activity. In this study, we reported a novel chiral organic donor-acceptor cocrystal based on asymmetrical components of benzo(b)naphtho(1,2-d)thiophene (BNT) and 9-oxo-9H-indeno(1,2-b)pyrazine-2,3-dicarbonitrile (DCAF) that exhibited red emission using a simple solution approach. During the self-assembly, a kinetically controlled growth of polar solvent or substrate induction led to the chiral packing and helical morphology twisted by the cooperation of electrostatic potential energy and chirality. Intriguingly, a "seeding-control" mechanism was newly developed for the production of c-BNT-DCAF helical crystals with a defined uniform chiral form, which enables chirality transfer and amplification from the microscopic to macroscopic level via supramolecular stacking. By introducing chiral additives or even a small break at the edge, the first nucleus acted as a chiral seeding to guide the donor/acceptor molecule alignment into the same handedness. A remarkably high dissymmetry factor (glum) value of 0.1 was demonstrated on the chiral manipulated ribbons, which is the highest among the reported charge-transfer complexes. This work offers us more paths for the design of chiral supramolecular systems for vital applications in organic optoelectronics, micro/nanomechanics, and biomimetics.
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Affiliation(s)
- Lei Yao
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Chen Pan
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Wenju Li
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jiacheng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yongyi Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Tao Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Guan Wang
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Peng Sheng
- Beijing Institute of Smart Energy, Beijing 102200, China
| | - Jing Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Xinyang Yin
- Beijing Institute of Smart Energy, Beijing 102200, China
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7
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Mejdrová I, Węgrzyn E, Carell T. Step-by-Step Towards Biological Homochirality - from Prebiotic Randomness To Perfect Asymmetry. Chem Asian J 2025; 20:e202401074. [PMID: 39400505 DOI: 10.1002/asia.202401074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 10/15/2024]
Abstract
The history of life's formation and the origin of its stereochemistry are nearly as multifaceted as the life itself. In this review, we focus on analyzing the step-by-step path leading to what we can define as "life" in parallel to what we know about the emergence of enantiomeric imbalance and subsequent transition to full homochirality. We start at the level of assembly of the building blocks of life from inorganic molecules and build up to the polymerization and formation of nucleic acids and peptides. We report and analyze different theories at various stages of this development and try to elucidate the most plausible theory.
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Affiliation(s)
- Ivana Mejdrová
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Ewa Węgrzyn
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
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8
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Casimo G, Micca Longo G, Longo S. Beyond Homochirality: Computer Modeling Hints of Heterochiral Proteins in Early and Extraterrestrial Life. ASTROBIOLOGY 2025; 25:22-31. [PMID: 39786977 DOI: 10.1089/ast.2024.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2025]
Abstract
Agent-based simulations are set to describe the early biotic selection of oligomers made of monomers of different chirality. The simulations consider the spatial distribution of agents and resources, the balance of biomass of different chirality, and the balance of chemical energy. Following the well-known Wald's hypothesis, a disadvantage is attributed to the change in chirality along the biochemical sequence. A racemic amino acid budget is considered, based on findings in meteorites and the results of Miller's experiments. It is also hypothesized that the very first life forms were heterotrophic. Given these assumptions, our simulations showed that biological sequences were not strictly homochiral and had few chirality changes. These results suggest that the current dominance of homochiral species may have been preceded by a more structurally varied biochemistry. This might be reflected in the few known heterochiral proteins, whose structures are based neither on alpha-helices nor on beta-sheets. Extraterrestrial life forms might be based on such heterochiral proteins.
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Affiliation(s)
- Gianluigi Casimo
- Dipartimento di Bioscienze, Biotecnologie e Ambientale, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Gaia Micca Longo
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Savino Longo
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Istituto per la Scienza e Tecnologia dei Plasmi - Consiglio Nazionale delle Ricerche, Bari, Italy
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9
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Ren J, Mathew A, Rodríguez-García M, Kohler T, Blacque O, Linden A, Eberl L, Sieber S, Gademann K. Functional biosynthetic stereodivergence in a gene cluster via a dihydrosydnone N-oxide. Commun Chem 2024; 7:301. [PMID: 39702669 DOI: 10.1038/s42004-024-01372-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 11/19/2024] [Indexed: 12/21/2024] Open
Abstract
Chirality plays a critical role in the biochemistry of life and often only one enantiomeric series is observed (homochirality). Only a few natural products have been obtained as racemates, e.g. the signalling molecule valdiazen produced by Burkholderia cenocepacia H111. In this study, we investigated the ham biosynthetic gene cluster and discovered that both the enantiomerically pure (R)-fragin and the racemic valdiazen result from the same pathway. This stereodivergence is based on the unusual heterocyclic intermediate dihydrosydnone N-oxide, as evident from gene knockout, stable isotope feeding experiments, and mass spectrometry experiments. Both non-enzymatic racemisation via keto-enol tautomerisation and enzyme-mediated dynamic kinetic resolution were found to be crucial to this stereodivergent pathway. This novel mechanism underpins the production of configurationally and biologically distinct metabolites from a single gene cluster. Our findings highlight the intricate design of an intertwined biosynthetic pathway and provide a deeper understanding of microbial secondary metabolism related to microbial communication.
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Affiliation(s)
- Jiajun Ren
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | - Tobias Kohler
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Olivier Blacque
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Anthony Linden
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
| | - Simon Sieber
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
| | - Karl Gademann
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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10
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Mirlohi K, Blocher McTigue WC. Coacervation for biomedical applications: innovations involving nucleic acids. SOFT MATTER 2024; 21:8-26. [PMID: 39641131 DOI: 10.1039/d4sm01253d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
Gene therapies, drug delivery systems, vaccines, and many other therapeutics, although seeing breakthroughs over the past few decades, still suffer from poor stability, biocompatibility, and targeting. Coacervation, a liquid-liquid phase separation phenomenon, is a pivotal technique increasingly employed to enhance the effectiveness of therapeutics. Through coacervation strategies, many current challenges in therapeutic formulations can be addressed due to the tunable nature of this technique. However, much remains to be explored to enhance these strategies further and scale them from the benchtop to industrial applications. In this review, we highlight the underlying mechanisms of coacervation, elucidating how factors such as pH, ionic strength, temperature, chirality, and charge patterning influence the formation of coacervates and the encapsulation of active ingredients. We then present a perspective on current strategies harnessing these systems, specifically for nucleic acid-based therapeutics. These include peptide-, protein-, and polymer-based approaches, nanocarriers, and hybrid methods, each offering unique advantages and challenges. Nucleic acid-based therapeutics are crucial for designing rapid responses to diseases, particularly in pandemics. While these exciting systems offer many advantages, they also present limitations and challenges which are explored in this work. Exploring coacervation in the biomedical frontier opens new avenues for innovative nucleic acid-based treatments, marking a significant stride towards advanced therapeutic solutions.
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Affiliation(s)
- Kimiasadat Mirlohi
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA.
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11
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Bagdžiūnas G. Can Chirality Answer Whether We Are Alone? Chirality 2024; 36:e23708. [PMID: 39054794 DOI: 10.1002/chir.23708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
Detecting biosignatures of life in extraterrestrial environments remains one of the primary objectives of scientific inquiry. Currently, both remote and direct detection methods are primarily aimed at identifying key molecular classes fundamental to terrestrial biology. However, a more universally applicable spectroscopic approach could involve searching for homochiral molecules. Thus, this perspective delves into the significance of homochirality as a critical factor in the origin of life. Without homochirality, the formation of self-recognizing and self-replicating complex molecules would be hindered. The various hypotheses concerning the origin of homochiral molecules have been explored and analyzed within this context. This perspective emphasizes the potential for discovering extraterrestrial microscopic life through the detection of homochiral molecules using chirodetecting methods such as chromatography and chiroptical spectroscopy or circular polarimetry as a promising remote technique. This discussion highlights the importance of homochirality in the broader search for life beyond Earth and underscores the need for innovative methodologies and instrumentation in astrobiological research. These techniques can be an effective method for detecting homochirality on future planetary missions.
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Affiliation(s)
- Gintautas Bagdžiūnas
- Group of Supramolecular Analysis, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
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12
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Deigin V, Linkova N, Vinogradova J, Vinogradov D, Polyakova V, Medvedev D, Krasichkov A, Volpina O. The First Reciprocal Activities of Chiral Peptide Pharmaceuticals: Thymogen and Thymodepressin, as Examples. Int J Mol Sci 2024; 25:5042. [PMID: 38732260 PMCID: PMC11084461 DOI: 10.3390/ijms25095042] [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: 03/15/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
Peptides show high promise in the targeting and intracellular delivery of next-generation biotherapeutics. The main limitation is peptides' susceptibility to proteolysis in biological systems. Numerous strategies have been developed to overcome this challenge by chemically enhancing the resistance to proteolysis. In nature, amino acids, except glycine, are found in L- and D-enantiomers. The change from one form to the other will change the primary structure of polypeptides and proteins and may affect their function and biological activity. Given the inherent chiral nature of biological systems and their high enantiomeric selectivity, there is rising interest in manipulating the chirality of polypeptides to enhance their biomolecular interactions. In this review, we discuss the first examples of up-and-down homeostasis regulation by two enantiomeric drugs: immunostimulant Thymogen (L-Glu-L-Trp) and immunosuppressor Thymodepressin (D-Glu(D-Trp)). This study shows the perspective of exploring chirality to remove the chiral wall between L- and D-biomolecules. The selected clinical result will be discussed.
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Affiliation(s)
- Vladislav Deigin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia; (V.D.); (O.V.)
| | - Natalia Linkova
- St. Petersburg Research Institute of Phthisiopulmonology, Ligovskii Prospect, 2-4, St. Petersburg 191036, Russia;
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
| | - Julia Vinogradova
- The Department of Hospital Therapy No. 2, I.M. Sechenov First Moscow State Medical University, 8 Trubetskaya Str., Building 2, Moscow 119991, Russia; (J.V.); (D.V.)
| | - Dmitrii Vinogradov
- The Department of Hospital Therapy No. 2, I.M. Sechenov First Moscow State Medical University, 8 Trubetskaya Str., Building 2, Moscow 119991, Russia; (J.V.); (D.V.)
| | - Victoria Polyakova
- St. Petersburg Research Institute of Phthisiopulmonology, Ligovskii Prospect, 2-4, St. Petersburg 191036, Russia;
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
| | - Dmitrii Medvedev
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
- The Department of Social Rehabilitation and Occupational Therapy of the St. Petersburg Medical and Social Institute, Kondratievsky St., 72A, St. Petersburg 195271, Russia
| | - Alexander Krasichkov
- Department of Radio Engineering Systems, Saint Petersburg Electrotechnical University ‘LETI’, St. Petersburg 197376, Russia
| | - Olga Volpina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia; (V.D.); (O.V.)
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13
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Hadidi M, Aghababaei F, Gonzalez-Serrano DJ, Goksen G, Trif M, McClements DJ, Moreno A. Plant-based proteins from agro-industrial waste and by-products: Towards a more circular economy. Int J Biol Macromol 2024; 261:129576. [PMID: 38253140 DOI: 10.1016/j.ijbiomac.2024.129576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
There is a pressing need for affordable, abundant, and sustainable sources of proteins to address the rising nutrient demands of a growing global population. The food and agriculture sectors produce significant quantities of waste and by-products during the growing, harvesting, storing, transporting, and processing of raw materials. These waste and by-products can sometimes be converted into valuable protein-rich ingredients with excellent functional and nutritional attributes, thereby contributing to a more circular economy. This review critically assesses the potential for agro-industrial wastes and by-products to contribute to global protein requirements. Initially, we discuss the origins and molecular characteristics of plant proteins derived from agro-industrial waste and by-products. We then discuss the techno-functional attributes, extraction methods, and modification techniques that are applied to these plant proteins. Finally, challenges linked to the safety, allergenicity, anti-nutritional factors, digestibility, and sensory attributes of plant proteins derived from these sources are highlighted. The utilization of agro-industrial by-products and wastes as an economical, abundant, and sustainable protein source could contribute towards achieving the Sustainable Development Agenda's 2030 goal of a "zero hunger world", as well as mitigating fluctuations in food availability and prices, which have detrimental impacts on global food security and nutrition.
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Affiliation(s)
- Milad Hadidi
- Department of Organic Chemistry, Faculty of Chemical Sciences and Technologies, University of Castilla-La Mancha, 13071 Ciudad Real, Spain; Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria.
| | | | - Diego J Gonzalez-Serrano
- Department of Organic Chemistry, Faculty of Chemical Sciences and Technologies, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Gulden Goksen
- Department of Food Technology, Vocational School of Technical Sciences at Mersin Tarsus Organized Industrial Zone, Tarsus University, Mersin, Turkey
| | - Monica Trif
- Food Research Department, Centre for Innovative Process Engineering (CENTIV) GmbH, 28816 Stuhr, Germany; CENCIRA Agrofood Research and Innovation Centre, Ion Mester 6, 400650 Cluj-Napoca, Romania
| | - David Julian McClements
- Department of Food Science, University of Massachusetts Amherst, 102 Holdsworth Way, Amherst, MA 01002, United States
| | - Andres Moreno
- Department of Organic Chemistry, Faculty of Chemical Sciences and Technologies, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
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14
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Deck LT, Hosseinalipour MS, Mazzotti M. Exact and Ubiquitous Condition for Solid-State Deracemization in Vitro and in Nature. J Am Chem Soc 2024; 146:3872-3882. [PMID: 38306469 PMCID: PMC10870780 DOI: 10.1021/jacs.3c11332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 02/04/2024]
Abstract
Solid-state deracemization is the amplification of an enantiomeric excess in suspensions of conglomerate-forming chiral compounds. Although numerous chemical and biochemical compounds deracemize, its governing mechanism has remained elusive. We introduce a novel formulation of the classical population-based model of deracemization through temperature cycles to prove that suspensions deracemize whenever a simple and ubiquitous condition is met: crystal dissolution must be faster than crystal growth. Such asymmetry is a known principle of crystallization, hence explaining the generality of deracemization. Through both experiments and a theoretical analysis, we demonstrate that this condition applies even for very small temperature cycles and for random temperature fluctuations. These findings establish solid-state deracemization as an attractive route to the manufacture of enantiopure products and as a plausible pathway toward the emergence of homochirality in nature.
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Affiliation(s)
- Leif-Thore Deck
- Institute of Energy and Process Engineering, ETH Zurich, Zurich 8092, Switzerland
| | | | - Marco Mazzotti
- Institute of Energy and Process Engineering, ETH Zurich, Zurich 8092, Switzerland
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15
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Luo Y, Liang M, Yu C, Ma W. Circular at the very beginning: on the initial genomes in the RNA world. RNA Biol 2024; 21:17-31. [PMID: 39016036 PMCID: PMC11259081 DOI: 10.1080/15476286.2024.2380130] [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] [Revised: 06/25/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
It is likely that an RNA world existed in early life, when RNA played both the roles of the genome and functional molecules, thereby undergoing Darwinian evolution. However, even with only one type of polymer, it seems quite necessary to introduce a labour division concerning these two roles because folding is required for functional molecules (ribozymes) but unfavourable for the genome (as a template in replication). Notably, while ribozymes tend to have adopted a linear form for folding without constraints, a circular form, which might have been topologically hindered in folding, seems more suitable for an RNA template. Another advantage of involving a circular genome could have been to resist RNA's end-degradation. Here, we explore the scenario of a circular RNA genome plus linear ribozyme(s) at the precellular stage of the RNA world through computer modelling. The results suggest that a one-gene scene could have been 'maintained', albeit with rather a low efficiency for the circular genome to produce the ribozyme, which required precise chain-break or chain-synthesis. This strict requirement may have been relieved by introducing a 'noncoding' sequence into the genome, which had the potential to derive a second gene through mutation. A two-gene scene may have 'run well' with the two corresponding ribozymes promoting the replication of the circular genome from different respects. Circular genomes with more genes might have arisen later in RNA-based protocells. Therefore, circular genomes, which are common in the modern living world, may have had their 'root' at the very beginning of life.
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Affiliation(s)
- Yufan Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Minglun Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chunwu Yu
- College of Computer Sciences, Wuhan University, Wuhan, China
| | - Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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16
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Gagnon JS, Hochberg D. Conditions for the origin of homochirality in primordial catalytic reaction networks. Sci Rep 2023; 13:9885. [PMID: 37336897 DOI: 10.1038/s41598-023-36852-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/11/2023] [Indexed: 06/21/2023] Open
Abstract
We study the generation of homochirality in a general chemical model (based on the homogeneous, fully connected Smoluchowski aggregation-fragmentation model) that obeys thermodynamics and can be easily mapped onto known origin of life models (e.g. autocatalytic sets, hypercycles, etc.), with essential aspects of origin of life modeling taken into consideration. Using a combination of theoretical modeling and numerical simulations, we look for minimal conditions for which our general chemical model exhibits spontaneous mirror symmetry breaking. We show that our model spontaneously breaks mirror symmetry in various catalytic configurations that only involve a small number of catalyzed reactions and nothing else. Of particular importance is that mirror symmetry breaking occurs in our model without the need for single-step autocatalytis or mutual inhibition, which may be of relevance for prebiotic chemistry.
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Affiliation(s)
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra. Ajalvir Km. 4, 28850, Torrejón de Ardóz, Madrid, Spain
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17
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Abstract
The nanoscale properties of nanomaterials, especially nanoparticles, including size, shape, and surface charge, have been extensively studied for their impact on nanomedicine. Given the inherent chiral nature of biological systems and their high enantiomeric selectivity, there is rising interest to manipulate the chirality of nanomaterials to enhance their biomolecular interactions and improve nanotherapeutics. Chiral nanostructures are currently more prevalently used in biosensing and diagnostic applications owing to their distinctive physical and optical properties, but they hold great promise for use in nanomedicine. In this Review, we first discuss stereospecific interactions between chiral nanomaterials and biomolecules before comparing the synthesis and characterization methods of chiral nanoparticles and nanoassemblies. Finally, we examine the applications of chiral nanotherapeutics in cancer, immunomodulation, and neurodegenerative diseases and propose plausible mechanisms in which chiral nanomaterials interact with cells for biological manipulation. This Review on chirality is a timely reminder of the arsenal of nanoscale modifications to boost research in nanotherapeutics.
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Affiliation(s)
- Yuwen Wang
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583
| | - Andy Tay
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583
- Institute of Health Innovation and Technology, National University of Singapore, Singapore 117599
- Tissue Engineering Program, National University of Singapore, Singapore 117510
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18
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Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway. Life (Basel) 2023; 13:life13030731. [PMID: 36983886 PMCID: PMC10053121 DOI: 10.3390/life13030731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.
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19
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Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells. Life (Basel) 2023; 13:life13020523. [PMID: 36836881 PMCID: PMC9966593 DOI: 10.3390/life13020523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/29/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a "membrane-stabilizing peptide" in RNA-based protocells-such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the "RNA gene" encoding this peptide may spread in the system owing to the peptide's function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes-here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a "nucleotide synthetase peptide" encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how "functional-takeover" in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a "promising" way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry.
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20
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Fundamental Cause of Bio-Chirality: Space-Time Symmetry—Concept Review. Symmetry (Basel) 2022. [DOI: 10.3390/sym15010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The search for fundamental determinants of bio-molecular chirality is a hot topic in biology, clarifying the meaning of evolution and the enigma of life’s origin. The question of origin may be resolved assuming that non-biological and biological entities obey nature’s universal laws grounded on space-time symmetry (STS) and space-time relativity (SPR). The fabric of STS is our review’s primary subject. This symmetry, encompassing the behavior of elementary particles and galaxy structure, imposes its fundamental laws on all hierarchical levels of the biological world. From the perspective of STS, objects across spatial scales may be classified as chiral or achiral concerning a specific space-related symmetry transformation: mirror reflection. The chiral object is not identical (i.e., not superimposable) to its mirror image. In geometry, distinguish two kinds of chiral objects. The first one does not have any reflective symmetry elements (a point or plane of symmetry) but may have rotational symmetry axes (dissymmetry). The second one does not have any symmetry elements (asymmetry). As the form symmetry deficiency, Chirality is the critical structural feature of natural systems, including sub-atomic particles and living matter. According to the Standard Model (SM) theory and String Theory (StrT), elementary particles associated with the four fundamental forces of nature determine the existence of micro- and galaxy scales of nature. Therefore, the inheritance of molecular symmetry from the symmetry of elementary particles indicates a bi-directional (internal [(micro-scale) and external (galaxy sale)] causal pathway of prevalent bio-chirality. We assume that the laws of the physical world impact the biological matter’s appearance through both extremities of spatial dimensions. The extended network of multi-disciplinary experimental evidence supports this hypothesis. However, many experimental results are derived and interpreted based on the narrow-view prerogative and highly specific terminology. The current review promotes a holistic approach to experimental results in two fast-developing, seemingly unrelated, divergent branches of STS and biological chirality. The generalized view on the origin of prevalent bio-molecular chirality is necessary for understanding the link between a diverse range of biological events. The chain of chirality transfer links ribosomal protein synthesis, cell morphology, and neuronal signaling with the laterality of cognitive functions.
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21
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Diniz PC, Wattis JAD, da Costa FP. Mathematical Models of Chiral Symmetry-breaking – A Review of General Theories, and Adiabatic Approximations of the APED System. ORIGINS LIFE EVOL B 2022; 52:183-204. [DOI: 10.1007/s11084-022-09631-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/17/2022] [Indexed: 11/25/2022]
Abstract
AbstractWe review the literature surrounding chiral symmetry-breaking in chemical systems, with a focus on understanding the mathematical models underlying these chemical processes. We comment in particular on the toy model of Sandars, Viedma’s crystal grinding systems and the APED model. We include a few new results based on asymptotic analysis of the APED system.
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22
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Savelieva EM, Zenchenko AA, Drenichev MS, Kozlova AA, Kurochkin NN, Arkhipov DV, Chizhov AO, Oslovsky VE, Romanov GA. In Planta, In Vitro and In Silico Studies of Chiral N6-Benzyladenine Derivatives: Discovery of Receptor-Specific S-Enantiomers with Cytokinin or Anticytokinin Activities. Int J Mol Sci 2022; 23:ijms231911334. [PMID: 36232653 PMCID: PMC9569578 DOI: 10.3390/ijms231911334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023] Open
Abstract
Cytokinins, classical phytohormones, affect all stages of plant ontogenesis, but their application in agriculture is limited because of the lack of appropriate ligands, including those specific for individual cytokinin receptors. In this work, a series of chiral N6-benzyladenine derivatives were studied as potential cytokinins or anticytokinins. All compounds contained a methyl group at the α-carbon atom of the benzyl moiety, making them R- or S-enantiomers. Four pairs of chiral nucleobases and corresponding ribonucleosides containing various substituents at the C2 position of adenine heterocycle were synthesized. A nucleophilic substitution reaction by secondary optically active amines was used. A strong influence of the chirality of studied compounds on their interaction with individual cytokinin receptors of Arabidopsis thaliana was uncovered in in vivo and in vitro assays. The AHK2 and CRE1/AHK4 receptors were shown to have low affinity for the studied S-nucleobases while the AHK3 receptor exhibited significant affinity for most of them. Thereby, three synthetic AHK3-specific cytokinins were discovered: N6-((S)-α-methylbenzyl)adenine (S-MBA), 2-fluoro,N6-((S)-α-methylbenzyl)adenine (S-FMBA) and 2-chloro,N6-((S)-α-methylbenzyl)adenine (S-CMBA). Interaction patterns between individual receptors and specific enantiomers were rationalized by structure analysis and molecular docking. Two other S-enantiomers (N6-((S)-α-methylbenzyl)adenosine, 2-amino,N6-((S)-α-methylbenzyl)adenosine) were found to exhibit receptor-specific and chirality-dependent anticytokinin properties.
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Affiliation(s)
- Ekaterina M. Savelieva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
| | - Anastasia A. Zenchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Mikhail S. Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Anna A. Kozlova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Nikolay N. Kurochkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Dmitry V. Arkhipov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
| | - Alexander O. Chizhov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky pr. 47, 119991 Moscow, Russia
| | - Vladimir E. Oslovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Georgy A. Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
- Correspondence: or
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23
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Takase H, Suga K, Matsune H, Umakoshi H, Shiomori K. Preferential adsorption of L-tryptophan by L-phospholipid coated porous polymer particles. Colloids Surf B Biointerfaces 2022; 216:112535. [PMID: 35594752 DOI: 10.1016/j.colsurfb.2022.112535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/25/2022] [Accepted: 05/01/2022] [Indexed: 11/28/2022]
Abstract
Chiral selective adsorption of L-amino acid, tryptophan (Trp) was achieved using phospholipid membrane-coated porous polymer particles (PPPs). PPPs with numerous pores were prepared by in situ polymerization of divinylbenzene, and then coated with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC, L-phospholipid) via the impregnation method. Elemental mapping of energy dispersive X-ray (EDX) analysis revealed that DPPC molecules were distributed to the surface and the inner part of PPPs, where almost all the DPPC molecules applied for impregnation were deposited on PPPs. The phospholipid membrane properties of DPPC-PPPs were characterized using the fluorescence probe 6-lauroyl-2-dimethylaminonaphthalene (Laurdan). The results show that DPPC-PPPs possessed a lipid membrane-like environment similar to pure DPPC liposomes, especially at temperatures below 35 °C. DPPC-PPPs slightly adsorbed L-Trp and D-Trp at 45 °C, while DPPC-PPPs significantly adsorbed L-Trp but not D-Trp at 30 °C: enantio excess (e.e.) was 75.0%. The time course of Trp adsorption was investigated: for both enantiomers, similar adsorption behaviors were observed for 30 h, thus suggesting surface adsorption onto DPPC-PPPs. L-Trp adsorption continued after 30 h, suggesting that L-Trp could be distributed in the inner part of DPPC-PPPs. Interestingly, the reused DPPC-PPPs featured improved adsorption performance, suggesting that the deposited DPPC membranes on PPPs could act as chiral selectors for L-Trp. The optical resolution of L-/D-Trp was performed using DPPC-PPPs, resulting in the e.e. of D-Trp was > 60%. Thus, DPPC-PPPs have the potential of chiral selective adsorption of L-amino acid, which can be used as chiral separation materials.
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Affiliation(s)
- Hayato Takase
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
| | - Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan; Department of Chemical Engineering, Tohoku University, 6-6-07 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hideki Matsune
- Department of Applied Chemistry, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 899-2192, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan.
| | - Koichiro Shiomori
- Department of Applied Chemistry, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 899-2192, Japan.
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24
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Sallembien Q, Bouteiller L, Crassous J, Raynal M. Possible chemical and physical scenarios towards biological homochirality. Chem Soc Rev 2022; 51:3436-3476. [PMID: 35377372 DOI: 10.1039/d1cs01179k] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.
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Affiliation(s)
- Quentin Sallembien
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Laurent Bouteiller
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Jeanne Crassous
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Matthieu Raynal
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
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25
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Dyakin VV, Uversky VN. Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality. Int J Mol Sci 2022; 23:ijms23073687. [PMID: 35409047 PMCID: PMC8998916 DOI: 10.3390/ijms23073687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Orangeburg, NY 10962, USA
- Correspondence:
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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26
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Abstract
The roots of biological homochirality remain unknown despite decades of study. A commonly proposed path includes an initial small enantiomeric excess that was amplified over time, but a satisfactory source of the excess and a plausible amplification process have yet to be described. We propose here a route to oligonucleotide homochirality from unactivated racemic sources based upon the facts that duplex structures are inherently homochiral and their synthesis from strands of complementary string nucleotide subunits is both uncommonly rapid and exergonic. Simulations employing available kinetic and thermochemical data in an iterated sequence of three equilibria in dry/wet cycles running from unactivated and racemic RNA monomers through oligonucleotides to duplex structures have shown that the exceptional association rate distorts the otherwise simple equilibrium string and overcomes the severe kinetic and stoichiometric barriers to the pairing of the statistically scant homochiral fractions. The simulations reveal widespread deracemization and the full conversion of racemic monomers to populations of L- and D-duplexes in a succession of growth in which the initially formed duplexes are replaced over time with increasingly larger descendants. This claim is open to experimental testing.
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Affiliation(s)
- David Ross
- Retired, formerly SRI International, Menlo Park, California, USA
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
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27
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Nemati A, Querciagrossa L, Callison C, Shadpour S, Nunes Gonçalves DP, Mori T, Cui X, Ai R, Wang J, Zannoni C, Hegmann T. Effects of shape and solute-solvent compatibility on the efficacy of chirality transfer: Nanoshapes in nematics. SCIENCE ADVANCES 2022; 8:eabl4385. [PMID: 35080976 PMCID: PMC8791610 DOI: 10.1126/sciadv.abl4385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Chirality, as a concept, is well understood at most length scales. However, quantitative models predicting the efficacy of the transmission of chirality across length scales are lacking. We propose here a modus operandi for a chiral nanoshape solute in an achiral nematic liquid crystal host showing that that chirality transfer may be understood by unusually simple geometric considerations. This mechanism is based on the product of a pseudoscalar chirality indicator and of a geometric shape compatibility factor based on the two-dimensional isoperimetric quotients for each nanoshape solute. The model is tested on an experimental set of precisely engineered gold nanoshapes. These libraries of calculated and in-parallel acquired experimental data among related nanoshapes pave the way for predictive calculations of chirality transfer in nanoscale, macromolecular, and biological systems, from designing chiral discriminators and enantioselective catalysts to developing chiral metamaterials and understanding nature's innate ability to transfer homochirality across length scales.
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Affiliation(s)
- Ahlam Nemati
- Materials Science Graduate Program, Kent State University, Kent, OH, USA
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, USA
| | - Lara Querciagrossa
- Dipartimento di Chimica Industriale and INSTM, Università di Bologna, Bologna, Italy
| | - Corinne Callison
- Materials Science Graduate Program, Kent State University, Kent, OH, USA
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, USA
| | - Sasan Shadpour
- Materials Science Graduate Program, Kent State University, Kent, OH, USA
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, USA
| | | | - Taizo Mori
- Institute for Solid State Physics, The University of Tokyo, Tokyo, Japan
| | - Ximin Cui
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ruoqi Ai
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jianfang Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Claudio Zannoni
- Dipartimento di Chimica Industriale and INSTM, Università di Bologna, Bologna, Italy
- Corresponding author. (C.Z.); (T.H.)
| | - Torsten Hegmann
- Materials Science Graduate Program, Kent State University, Kent, OH, USA
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, USA
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
- Brain Health Research Institute, Kent State University, Kent, OH, USA
- Corresponding author. (C.Z.); (T.H.)
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28
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Symmetry of Post-Translational Modifications in a Human Enzyme. Symmetry (Basel) 2022. [DOI: 10.3390/sym14020212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Paraoxonase 2 (PON2) is a member of a small family of human lactonases. Recently, post-translational modifications (PTMs) of PON2 were highlighted, one of which involved the modulation of the enzyme activity. Furthermore, two important single nucleotide polymorphisms (SNPs) involved in type 2 diabetes and its consequences, were found to modulate the enzyme activity as well. The position on the PON2 structural model of both residues corresponding to SNPs and PTMs suggested a symmetry of the molecule. By sequence and structure superposition we were able to confirm this finding. The result will be discussed in light of the evolution of symmetry in biological molecules and their function.
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29
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Gillet J, Rongy L, De Decker Y. Spontaneous mirror symmetry breaking in reaction–diffusion systems: ambivalent role of the achiral precursor. Phys Chem Chem Phys 2022; 24:26144-26155. [DOI: 10.1039/d2cp03102g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reaction–diffusion simulations reveal that the achiral substrate concentration may play an ambivalent role in spontaneous mirror symmetry breaking.
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Affiliation(s)
- Jean Gillet
- Nonlinear Physical, Chemistry Unit, CP-231, Université libre de Bruxelles (ULB), 1050 Bruxelles, Belgium
| | - Laurence Rongy
- Nonlinear Physical, Chemistry Unit, CP-231, Université libre de Bruxelles (ULB), 1050 Bruxelles, Belgium
| | - Yannick De Decker
- Nonlinear Physical, Chemistry Unit, CP-231, Université libre de Bruxelles (ULB), 1050 Bruxelles, Belgium
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30
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Liang Y, Yu C, Ma W. The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life. PLoS Comput Biol 2021; 17:e1009761. [PMID: 34965249 PMCID: PMC8752021 DOI: 10.1371/journal.pcbi.1009761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/11/2022] [Accepted: 12/15/2021] [Indexed: 11/19/2022] Open
Abstract
The origin of life involved complicated evolutionary processes. Computer modeling is a promising way to reveal relevant mechanisms. However, due to the limitation of our knowledge on prebiotic chemistry, it is usually difficult to justify parameter-setting for the modeling. Thus, typically, the studies were conducted in a reverse way: the parameter-space was explored to find those parameter values “supporting” a hypothetical scene (that is, leaving the parameter-justification a later job when sufficient knowledge is available). Exploring the parameter-space manually is an arduous job (especially when the modeling becomes complicated) and additionally, difficult to characterize as regular “Methods” in a paper. Here we show that a machine-learning-like approach may be adopted, automatically optimizing the parameters. With this efficient parameter-exploring approach, the evolutionary modeling on the origin of life would become much more powerful. In particular, based on this, it is expected that more near-reality (complex) models could be introduced, and thereby theoretical research would be more tightly associated with experimental investigation in this field–hopefully leading to significant steps forward in respect to our understanding on the origin of life. People have long been interested in the evolutionary processes through which life on our planet could have arisen from a non-life background. However, it seems that experimental studies in this field are proceeding slowly, perhaps owing to the complication of such processes. In the meantime, computer modeling has shown its potential to disclose the evolutionary mechanisms involved. Now a major difficulty of the computer modeling work is to justify the parameter-setting–on account of our limited knowledge on prebiotic chemistry and environments. Thus, people tend to explore the parameter space to seek parameter values in favor of the hypothetic scene and leave the parameter-justification a later job when sufficient knowledge is available. To date, the parameter-exploration is usually conducted manually (in many cases by trial and error), thus arduous and unpredictable. Inspired by the algorithm of machine-learning, we designed an automatic approach of parameter-exploration. The results showed that the approach is quite effective–that is, “good” parameter-sets in favor of hypothetic scenes in the origin of life can be found automatically. It is expected that such a machine-learning-like method would greatly enhance the efficiency of our evolutionary modeling studies on the origin of life in future.
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Affiliation(s)
- Yuzhen Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chunwu Yu
- College of Computer Sciences, Wuhan University, Wuhan, China
| | - Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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31
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Dantsu Y, Zhang Y, Zhang W. Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness. Genes (Basel) 2021; 13:46. [PMID: 35052385 PMCID: PMC8774879 DOI: 10.3390/genes13010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/19/2022] Open
Abstract
Nucleic-acid-based small molecule and oligonucleotide therapies are attractive topics due to their potential for effective target of disease-related modules and specific control of disease gene expression. As the non-naturally occurring biomolecules, modified DNA/RNA nucleoside and oligonucleotide analogues composed of L-(deoxy)riboses, have been designed and applied as innovative therapeutics with superior plasma stability, weakened cytotoxicity, and inexistent immunogenicity. Although all the chiral centers in the backbone are mirror converted from the natural D-nucleic acids, L-nucleic acids are equipped with the same nucleobases (A, G, C and U or T), which are critical to maintain the programmability and form adaptable tertiary structures for target binding. The types of L-nucleic acid drugs are increasingly varied, from chemically modified nucleoside analogues that interact with pathogenic polymerases to nanoparticles containing hundreds of repeating L-nucleotides that circulate durably in vivo. This article mainly reviews three different aspects of L-nucleic acid therapies, including pharmacological L-nucleosides, Spiegelmers as specific target-binding aptamers, and L-nanostructures as effective drug-delivery devices.
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Affiliation(s)
- Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
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32
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John N, Mariamma AT. Recent developments in the chiroptical properties of chiral plasmonic gold nanostructures: bioanalytical applications. Mikrochim Acta 2021; 188:424. [PMID: 34811580 PMCID: PMC8608422 DOI: 10.1007/s00604-021-05066-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/14/2021] [Indexed: 11/25/2022]
Abstract
The presence of excess L-amino acid in the Murchison meteorite, circular polarization effect in the genesis of stars and existence of chirality in interstellar molecules contribute to the origin of life on earth. Chiral-sensitive techniques have been employed to untangle the secret of the symmetries of the universe, designing of effective secure drugs and investigation of chiral biomolecules. The relationship between light and chiral molecules was employed to probe and explore such molecules using spectroscopy techniques. The mutual interaction between electromagnetic spectrum and chirality of matter give rise to distinct optical response, which advances vital information contents in chiroptical spectroscopy. Chiral plasmonic gold nanoparticle exhibits distinctive circular dichroism peaks in broad wavelength range thereby crossing the limits of its characterization. The emergence of strong optical activity of gold nanosystem is related to its high polarizability, resulting in plasmonic and excitonic effects on incident photons. Inspired by the development of advanced chiral plasmonic nanomaterials and exploring its properties, this review gives an overview of various chiral gold nanostructures and the mechanism behind its chiroptical properties. Finally, we highlight the application of different chiral gold nanomaterials in the field of catalysis and medical applications with special emphasis to biosensing and biodetection.
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Affiliation(s)
- Nebu John
- The Post Graduate and Research Department of Chemistry, Mar Thoma College, Mahatma Gandhi University, Tiruvalla, 689103 Kerala India
| | - Anslin Thankachan Mariamma
- The Post Graduate Department of Mathematics, St. Gregorios College, University of Kerala, Kottarakara, 691531 Kerala India
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33
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Verma G, Mehta R, Kumar S, Ma S. Metal‐Organic Frameworks as a New Platform for Enantioselective Separations. Isr J Chem 2021. [DOI: 10.1002/ijch.202100073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gaurav Verma
- Department of Chemistry University of North Texas 1508 W Mulberry St Denton, TX 76201 USA
| | - Ruhi Mehta
- Department of Chemistry Multani Mal Modi College Patiala 147001 Punjab India
| | - Sanjay Kumar
- Department of Chemistry Multani Mal Modi College Patiala 147001 Punjab India
| | - Shengqian Ma
- Department of Chemistry University of North Texas 1508 W Mulberry St Denton, TX 76201 USA
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34
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Richert C, Doppleb O, Bremer J, Bechthold M, Sánchez Rico C, Göhringer D, Griesser H. Determining the Diastereoselectivity of the Formation of Dipeptidonucleotides by NMR Spectroscopy. Chemistry 2021; 27:13544-13551. [PMID: 34292623 PMCID: PMC8518831 DOI: 10.1002/chem.202101630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Indexed: 12/02/2022]
Abstract
Proteins are composed of l‐amino acids, but nucleic acids and most oligosaccharides contain d‐sugars as building blocks. It is interesting to ask whether this is a coincidence or a consequence of the functional interplay of these biomolecules. One reaction that provides an opportunity to study this interplay is the formation of phosphoramidate‐linked peptido RNA from amino acids and ribonucleotides in aqueous condensation buffer. Here we report how the diastereoselectivity of the first peptide coupling of the peptido RNA pathway can be determined in situ by NMR spectroscopy. When a racemic mixture of an amino acid ester was allowed to react with an 5′‐aminoacidyl nucleotide, diastereomeric ratios of up to 72 : 28 of the resulting dipeptido nucleotides were found by integration of 31P‐ or 1H‐NMR peaks. The highest diastereomeric excess was found for the homochiral coupling product d‐Ser‐d‐Trp, phosphoramidate‐linked to adenosine 5′‐monophosphate with its d‐ribose ring. When control reactions with an N‐acetyl amino acid and valine methyl ester were run in organic solvent, the diastereoselectivity was found to be lower, with diastereomeric ratios≤62 : 38. The results from the exploratory study thus indicate that the ribonucleotide residue not only facilitates the coupling of lipophilic amino acids in aqueous medium but also the formation of a homochiral dipeptide. The methodology described here may be used to search for other stereoselective reactions that shed light on the origin of homochirality.
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Affiliation(s)
- Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, GERMANY
| | - Olivia Doppleb
- University of Stuttgart: Universitat Stuttgart, Chemistry, GERMANY
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35
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Ramesh V, Krishnan J. Symmetry breaking meets multisite modification. eLife 2021; 10:65358. [PMID: 34018920 PMCID: PMC8439660 DOI: 10.7554/elife.65358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/20/2021] [Indexed: 12/19/2022] Open
Abstract
Multisite modification is a basic way of conferring functionality to proteins and a key component of post-translational modification networks. Additional interest in multisite modification stems from its capability of acting as complex information processors. In this paper, we connect two seemingly disparate themes: symmetry and multisite modification. We examine different classes of random modification networks of substrates involving separate or common enzymes. We demonstrate that under different instances of symmetry of the modification network (invoked explicitly or implicitly and discussed in the literature), the biochemistry of multisite modification can lead to the symmetry being broken. This is shown computationally and consolidated analytically, revealing parameter regions where this can (and in fact does) happen, and characteristics of the symmetry-broken state. We discuss the relevance of these results in situations where exact symmetry is not present. Overall, through our study we show how symmetry breaking (i) can confer new capabilities to protein networks, including concentration robustness of different combinations of species (in conjunction with multiple steady states); (ii) could have been the basis for ordering of multisite modification, which is widely observed in cells; (iii) can significantly impact information processing in multisite modification and in cell signalling networks/pathways where multisite modification is present; and (iv) can be a fruitful new angle for engineering in synthetic biology and chemistry. All in all, the emerging conceptual synthesis provides a new vantage point for the elucidation and the engineering of molecular systems at the junction of chemical and biological systems. Proteins help our cells perform the chemical reactions necessary for life. Once proteins are made, they can also be modified in different ways. This can simply change their activity, or otherwise make them better suited for their specific jobs within the cell. Biological ‘catalysts’ called enzymes carry out protein modifications by reversibly adding (or removing) chemical groups, such as phosphate groups. ‘Multisite modifications’ occur when a protein has two or more modifications in different areas, which can be added randomly or in a specific sequence. The combination of all the modifications attached to a protein acts like a chemical barcode and confers a specific function to the protein. Modification networks add levels of complexity above individual proteins. These encompass not only the proteins in a cell or tissue, but also the different enzymes that can modify them, and how they all interact with each other. Although our knowledge of these networks is substantial, basic aspects, such as how the ordering of multisite modification systems emerges, is still not well understood. Using a simple set of multisite modifications, Ramesh and Krishnan set out to study the potential mechanisms allowing the creation of order in this context. Symmetry is a pervasive theme across the sciences. In biology, symmetry and how it may be broken, is important to understand, for example, how organism develop. Ramesh and Krishnan used the perspective of symmetry in protein networks to uncover the origins of ordering. First, mathematical models of simple modification networks were created based on their basic descriptions. This system centred on proteins that could have phosphate modifications at two possible sites. The network was ‘symmetric’, meaning that the rate of different sets of chemical reactions was identical, as were the amounts of all the enzymes involved. Dissecting the simulated network using a variety of mathematical approaches showed that its initial symmetry could break, giving rise to sets of ordered multisite modifications. Breaking symmetry did not require any additional features or factors; the basic chemical ‘ingredients’ of protein modification were all that was needed. The prism of symmetry also revealed other aspects of these multisite modification networks, such as robustness and oscillations. This study sheds new light on the mechanism behind ordering of protein modifications. In the future, Ramesh and Krishnan hope that this approach can be applied to the study of not just proteins but also a wider range of biochemical networks.
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Affiliation(s)
- Vaidhiswaran Ramesh
- Department of Chemical Engineerng, Centre for Process Systems Engineering, Imperial College London, London, United Kingdom
| | - J Krishnan
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London, United Kingdom
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36
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Chu XY, Zhang HY. Protein Homochirality May Be Derived from Primitive Peptide Synthesis by RNA. ASTROBIOLOGY 2021; 21:628-635. [PMID: 33600215 DOI: 10.1089/ast.2020.2324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Homochirality is a feature of life, but its origin is still disputed. Recent theories indicate that the origin of homochirality coincided with that of the RNA world, but proteins have not yet been incorporated into the story. Ribosome is considered a living fossil that survived the RNA world and records the oldest interaction between RNA and proteins. Inspired by several ribosome-related findings, we propose a hypothesis as follows: the substrate chirality preference of some primitive peptide synthesis ribozymes can mediate the chirality transmission from RNA to protein. In return, the chiral preference of protective peptide-RNA interaction can bring these ribozymes an evolutionary advantage and facilitate the expansion of enantiomeric excess in peptides. Monte Carlo simulation results show that this system's chemistry model is plausible. This model can be further tested through investigation of the chirality preference for the interactions between d/l-ribose-composed rRNA homologs and l/d-amino acid-composed peptides.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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37
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Liu J, Shadpour S, Prévôt ME, Chirgwin M, Nemati A, Hegmann E, Lemieux RP, Hegmann T. Molecular Conformation of Bent-Core Molecules Affected by Chiral Side Chains Dictates Polymorphism and Chirality in Organic Nano- and Microfilaments. ACS NANO 2021; 15:7249-7270. [PMID: 33734664 DOI: 10.1021/acsnano.1c00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The coupling between molecular conformation and chirality is a cornerstone in the construction of supramolecular helical structures of small molecules across various length scales. Inspired by biological systems, conformational preselection and control in artificial helical molecules, polymers, and aggregates has guided various applications in optics, photonics, and chiral sorting among others, which are frequently based on an inherent chirality amplification through processes such as templating and self-assembly. The so-called B4 nano- or microfilament phase formed by some bent-shaped molecules is an exemplary case for such chirality amplification across length scales, best illustrated by the formation of distinct nano- or microscopic chiral morphologies controlled by molecular conformation. Introduction of one or more chiral centers in the aliphatic side chains led to the discovery of homochiral helical nanofilament, helical microfilament, and heliconical-layered nanocylinder morphologies. Herein, we demonstrate how a priori calculations of the molecular conformation affected by chiral side chains are used to design bent-shaped molecules that self-assemble into chiral nano- and microfilament as well as nanocylinder conglomerates despite the homochiral nature of the molecules. Furthermore, relocation of the chiral center leads to formation of helical as well as flat nanoribbons. Self-consistent data sets from polarized optical as well as scanning and transmission electron microscopy, thin-film and solution circular dichroism spectropolarimetry, and synchrotron-based X-ray diffraction experiments support the progressive and predictable change in morphology controlled by structural changes in the chiral side chains. The formation of these morphologies is discussed in light of the diminishing effects of molecular chirality as the chain length increases or as the chiral center is moved away from the core-chain juncture. The type of phase (B1-columnar or B4) and morphology of the nano- or microfilaments generated can further be controlled by sample treatment conditions such as by the cooling rate from the isotropic melt or by the presence of an organic solvent in the ensuing colloidal dispersions. We show that these nanoscale morphologies can then organize into a wealth of two- and three-dimensional shapes and structures ranging from flower blossoms to fiber mats formed by intersecting flat nanoribbons.
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Affiliation(s)
- Jiao Liu
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Sasan Shadpour
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Marianne E Prévôt
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Michael Chirgwin
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Ahlam Nemati
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Elda Hegmann
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242-0001, United States
- Brain Health Research Institute, Kent State University, Kent, Ohio 44242-0001, United States
| | - Robert P Lemieux
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Torsten Hegmann
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242-0001, United States
- Brain Health Research Institute, Kent State University, Kent, Ohio 44242-0001, United States
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242-0001, United States
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38
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Buhse T, Cruz JM, Noble-Terán ME, Hochberg D, Ribó JM, Crusats J, Micheau JC. Spontaneous Deracemizations. Chem Rev 2021; 121:2147-2229. [DOI: 10.1021/acs.chemrev.0c00819] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Thomas Buhse
- Centro de Investigaciones Químicas−IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, 62209 Cuernavaca, Morelos Mexico
| | - José-Manuel Cruz
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, Tuxtla Gutiérrez, Chiapas 29050, Mexico
| | - María E. Noble-Terán
- Centro de Investigaciones Químicas−IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, 62209 Cuernavaca, Morelos Mexico
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera Ajalvir, Km. 4, 28850 Torrejón de Ardoz, Madrid Spain
| | - Josep M. Ribó
- Institut de Ciències del Cosmos (IEEC-ICC) and Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalunya Spain
| | - Joaquim Crusats
- Institut de Ciències del Cosmos (IEEC-ICC) and Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalunya Spain
| | - Jean-Claude Micheau
- Laboratoire des IMRCP, UMR au CNRS No. 5623, Université Paul Sabatier, F-31062 Toulouse Cedex, France
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Mirror Symmetry Breaking in Liquids and Their Impact on the Development of Homochirality in Abiogenesis: Emerging Proto-RNA as Source of Biochirality? Symmetry (Basel) 2020. [DOI: 10.3390/sym12071098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recent progress in mirror symmetry breaking and chirality amplification in isotropic liquids and liquid crystalline cubic phases of achiral molecule is reviewed and discussed with respect to its implications for the hypothesis of emergence of biological chirality. It is shown that mirror symmetry breaking takes place in fluid systems where homochiral interactions are preferred over heterochiral and a dynamic network structure leads to chirality synchronization if the enantiomerization barrier is sufficiently low, i.e., that racemization drives the development of uniform chirality. Local mirror symmetry breaking leads to conglomerate formation. Total mirror symmetry breaking requires either a proper phase transitions kinetics or minor chiral fields, leading to stochastic and deterministic homochirality, respectively, associated with an extreme chirality amplification power close to the bifurcation point. These mirror symmetry broken liquids are thermodynamically stable states and considered as possible systems in which uniform biochirality could have emerged. A model is hypothesized, which assumes the emergence of uniform chirality by chirality synchronization in dynamic “helical network fluids” followed by polymerization, fixing the chirality and leading to proto-RNA formation in a single process.
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