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Andersen JL, Fagerberg R, Flamm C, Fontana W, Kolčák J, Laurent CVFP, Merkle D, Nøjgaard N. Representing Catalytic Mechanisms with Rule Composition. J Chem Inf Model 2022; 62:5513-5524. [PMID: 36326605 DOI: 10.1021/acs.jcim.2c00426] [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
An "imaginary transition structure" overlays the molecular graphs of the educt and product sides of an elementary chemical reaction in a single graph to highlight the changes in bond structure. We generalize this idea to reactions with complex mechanisms in a formally rigorous approach based on composing arrow-pushing steps represented as graph-transformation rules to construct an overall composite rule and a derived transition structure. This transition structure retains information about transient bond changes that are invisible at the overall level and can be constructed automatically from an existing database of detailed enzymatic mechanisms. We use the construction to (i) illuminate the distribution of catalytic action across enzymes and substrates and (ii) to search in a large database for reactions of known or unknown mechanisms that are compatible with the mechanism captured by the constructed composite rule.
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Affiliation(s)
- Jakob L Andersen
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Rolf Fagerberg
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Christoph Flamm
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Walter Fontana
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Juri Kolčák
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.,Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Christophe V F P Laurent
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Daniel Merkle
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Nikolai Nøjgaard
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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2
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Sharma S, Arya A, Cruz R, Cleaves II HJ. Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives. Life (Basel) 2021; 11:1140. [PMID: 34833016 PMCID: PMC8624352 DOI: 10.3390/life11111140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species. Such complex systems may have given rise to emergent phenomena that ultimately led to the origin of life on Earth. The environmental conditions and processes involved in this emergence may not be fully recapitulable, making it difficult for experimentalists to study prebiotic systems in laboratory simulations. Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life. Here, we review tools and techniques for modelling prebiotic chemical reaction networks and outline possible ways to identify self-replicating features that are central to many origin-of-life models.
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Affiliation(s)
- Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Department of Biochemistry, Deshbandhu College, University of Delhi, New Delhi 110019, India
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Aayush Arya
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Department of Physics, Lovely Professional University, Jalandhar-Delhi GT Road, Phagwara 144001, India
| | - Romulo Cruz
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Big Data Laboratory, Information and Communications Technology Center (CTIC), National University of Engineering, Amaru 210, Lima 15333, Peru
| | - Henderson James Cleaves II
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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3
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Tran QP, Adam ZR, Fahrenbach AC. Prebiotic Reaction Networks in Water. Life (Basel) 2020; 10:E352. [PMID: 33339192 PMCID: PMC7765580 DOI: 10.3390/life10120352] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/05/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
A prevailing strategy in origins of life studies is to explore how chemistry constrained by hypothetical prebiotic conditions could have led to molecules and system level processes proposed to be important for life's beginnings. This strategy has yielded model prebiotic reaction networks that elucidate pathways by which relevant compounds can be generated, in some cases, autocatalytically. These prebiotic reaction networks provide a rich platform for further understanding and development of emergent "life-like" behaviours. In this review, recent advances in experimental and analytical procedures associated with classical prebiotic reaction networks, like formose and Miller-Urey, as well as more recent ones are highlighted. Instead of polymeric networks, i.e., those based on nucleic acids or peptides, the focus is on small molecules. The future of prebiotic chemistry lies in better understanding the genuine complexity that can result from reaction networks and the construction of a centralised database of reactions useful for predicting potential network evolution is emphasised.
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Affiliation(s)
| | - Zachary R. Adam
- Department of Planetary Sciences, University of Arizona, Tucson, AZ 85721, USA;
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Wołos A, Roszak R, Żądło-Dobrowolska A, Beker W, Mikulak-Klucznik B, Spólnik G, Dygas M, Szymkuć S, Grzybowski BA. Synthetic connectivity, emergence, and
self-regeneration in the network of prebiotic
chemistry. Science 2020; 369:369/6511/eaaw1955. [DOI: 10.1126/science.aaw1955] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/28/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
The challenge of prebiotic chemistry is to
trace the syntheses of life’s key building blocks
from a handful of primordial substrates. Here we
report a forward-synthesis algorithm that
generates a full network of prebiotic chemical
reactions accessible from these substrates under
generally accepted conditions. This network
contains both reported and previously unidentified
routes to biotic targets, as well as plausible
syntheses of abiotic molecules. It also exhibits
three forms of nontrivial chemical emergence, as
the molecules within the network can act as
catalysts of downstream reaction types; form
functional chemical systems, including
self-regenerating cycles; and produce surfactants
relevant to primitive forms of biological
compartmentalization. To support these claims,
computer-predicted, prebiotic syntheses of several
biotic molecules as well as a multistep,
self-regenerative cycle of iminodiacetic acid were
validated by experiment.
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Affiliation(s)
- Agnieszka Wołos
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Rafał Roszak
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | | | - Wiktor Beker
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Barbara Mikulak-Klucznik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Grzegorz Spólnik
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Mirosław Dygas
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
| | - Sara Szymkuć
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry,
Polish Academy of Sciences, Warsaw,
Poland
- Allchemy, Inc., Highland, IN,
USA
- Center for Soft and Living Matter of
Korea’s Institute for Basic Science (IBS), Ulsan,
South Korea
- Department of Chemistry, Ulsan
National Institute of Science and Technology,
Ulsan, South Korea
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Andersen JL, Flamm C, Merkle D, Stadler PF. Chemical Transformation Motifs-Modelling Pathways as Integer Hyperflows. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:510-523. [PMID: 29990045 DOI: 10.1109/tcbb.2017.2781724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to reactions. Pathways are modelled as integer hyperflows and we expand the network model by detailed routing constraints. In contrast to the more traditional approaches like Flux Balance Analysis or Elementary Mode analysis we insist on integer-valued flows. While this choice makes it necessary to solve possibly hard integer linear programs, it has the advantage that more detailed mechanistic questions can be formulated. It is thus possible to query networks for general transformation motifs, and to automatically enumerate optimal and near-optimal pathways. Similarities and differences between our work and traditional approaches in metabolic network analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimized. We then use a model of sugar chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest.
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Tsanakopoulou M, Sutherland JD. Cyanamide as a prebiotic phosphate activating agent - catalysis by simple 2-oxoacid salts. Chem Commun (Camb) 2018; 53:11893-11896. [PMID: 29043309 PMCID: PMC5708344 DOI: 10.1039/c7cc07517k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyanamide is a prebiotically plausible compound that has previously been invoked as a phosphate activating agent. However, its reactions with phosphate monoesters are very slow and tend to be low yielding. We now report a fast and efficient phosphate activation reaction using cyanamide in the presence of glyoxylate or pyruvate. These simple 2-oxoacid salts are shown to function as catalysts and in an optimised system, adenosine-3'-phosphate was converted to adenosine-2',3'-cyclic phosphate in 95% yield.
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Affiliation(s)
- Maria Tsanakopoulou
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, UK.
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, UK.
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Meringer M, Cleaves HJ. Exploring astrobiology using in silico molecular structure generation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0344. [PMID: 29133444 PMCID: PMC5686402 DOI: 10.1098/rsta.2016.0344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 05/27/2023]
Abstract
The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, 'animate' matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic 'chemical space'. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of 'chemical spaces' beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Markus Meringer
- Earth Observation Center (EOC), German Aerospace Center (DLR), Münchner Straße 20, 82234 Oberpfaffenhofen-Wessling, Germany
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-IE-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Institute for Advanced Study, Princeton, NJ 08540, USA
- Blue Marble Space Institute of Science, 1515 Gallatin Street NW, Washington, DC 20011, USA
- Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Meringer M, Cleaves HJ. Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents. Sci Rep 2017; 7:17540. [PMID: 29235498 PMCID: PMC5727506 DOI: 10.1038/s41598-017-17345-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/23/2017] [Indexed: 11/16/2022] Open
Abstract
The reverse tricarboxylic acid (rTCA) cycle has been explored from various standpoints as an idealized primordial metabolic cycle. Its simplicity and apparent ubiquity in diverse organisms across the tree of life have been used to argue for its antiquity and its optimality. In 2000 it was proposed that chemoinformatics approaches support some of these views. Specifically, defined queries of the Beilstein database showed that the molecules of the rTCA are heavily represented in such compound databases. We explore here the chemical structure “space,” e.g. the set of organic compounds which possesses some minimal set of defining characteristics, of the rTCA cycle’s intermediates using an exhaustive structure generation method. The rTCA’s chemical space as defined by the original criteria and explored by our method is some six to seven times larger than originally considered. Acknowledging that each assumption in what is a defining criterion making the rTCA cycle special limits possible generative outcomes, there are many unrealized compounds which fulfill these criteria. That these compounds are unrealized could be due to evolutionary frozen accidents or optimization, though this optimization may also be for systems-level reasons, e.g., the way the pathway and its elements interface with other aspects of metabolism.
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Affiliation(s)
- Markus Meringer
- German Aerospace Center (DLR), Earth Observation Center (EOC), Münchner Straße 20, D-82234, Oberpfaffenhofen-Wessling, Germany
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan. .,The Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ, 08540, USA. .,Blue Marble Space Institute of Science, 1515 Gallatin St. NW, Washington, DC, 20011, USA. .,Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, Georgia.
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Chemical Transformations in Proto-Cytoplasmic Media. Phosphorus Coupling in the Silica Hydrogel Phase. Life (Basel) 2017; 7:life7040045. [PMID: 29156594 PMCID: PMC5745558 DOI: 10.3390/life7040045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/12/2017] [Accepted: 10/27/2017] [Indexed: 01/03/2023] Open
Abstract
It has been proposed that prebiotic chemical studies on the emergence of primitive life would be most relevant when performed in a hydrogel, rather than an aqueous, environment. In this paper we describe the ambient temperature coupling of phosphorus oxyacids [Pi] mediated by Fe(II) under aerobic conditions within a silica hydrogel (SHG) environment. We have chosen to examine SHGs as they have considerable geological precedence as key phases in silicification en route to rock formation. Following a description of the preparation and characterization studies on our SHG formulations, coupling experiments between Pi species are described across multiple permutations of (i) Pi compound; (ii) gel formulation; (iii) metal salt additive; and (iv) pH-modifying agent. The results suggest that successful Pi coupling, indicated by observation of pyrophosphate [PPi(V)] via 31P-NMR spectroscopy, takes place when the following components are present: (i) a mixture of mixture of Pi(III) and Pi(V) or pure PPi(III– V); (ii) Fe(II); (iii) acetic or formic acid (not hydrochloric acid); (iv) aerobic conditions or the presence of H2O2 as an oxidant; and (v) the presence of a gel system. On the basis of these, and aqueous control reactions, we suggest mechanistic possibilities.
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Richter C, Berndt F, Kunde T, Mahrwald R. Decarboxylative Cascade Reactions of Dihydroxyfumaric Acid: A Preparative Approach to the Glyoxylate Scenario. Org Lett 2016; 18:2950-3. [DOI: 10.1021/acs.orglett.6b01287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Celin Richter
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Falko Berndt
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Tom Kunde
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Rainer Mahrwald
- Institute of Chemistry, Humboldt-University, Brook-Taylor Str. 2, 12489 Berlin, Germany
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