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Arya A, Ray J, Sharma S, Cruz Simbron R, Lozano A, Smith HB, Andersen JL, Chen H, Meringer M, Cleaves HJ. An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions. Chem Sci 2022; 13:4838-4853. [PMID: 35655880 PMCID: PMC9067619 DOI: 10.1039/d2sc00256f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/16/2022] [Indexed: 11/21/2022] Open
Abstract
A central question in origins of life research is how non-entailed chemical processes, which simply dissipate chemical energy because they can do so due to immediate reaction kinetics and thermodynamics, enabled the origin of highly-entailed ones, in which concatenated kinetically and thermodynamically favorable processes enhanced some processes over others. Some degree of molecular complexity likely had to be supplied by environmental processes to produce entailed self-replicating processes. The origin of entailment, therefore, must connect to fundamental chemistry that builds molecular complexity. We present here an open-source chemoinformatic workflow to model abiological chemistry to discover such entailment. This pipeline automates generation of chemical reaction networks and their analysis to discover novel compounds and autocatalytic processes. We demonstrate this pipeline's capabilities against a well-studied model system by vetting it against experimental data. This workflow can enable rapid identification of products of complex chemistries and their underlying synthetic relationships to help identify autocatalysis, and potentially self-organization, in such systems. The algorithms used in this study are open-source and reconfigurable by other user-developed workflows.
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Affiliation(s)
- Aayush Arya
- Department of Physics, Lovely Professional University Jalandhar Delhi-GT Road Phagwara Punjab 144411 India
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
| | - Jessica Ray
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
| | - Siddhant Sharma
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Department of Biochemistry, Deshbandhu College, University of Delhi New Delhi 110019 India
| | - Romulo Cruz Simbron
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Laboratorio de Investigación Fisicoquímica (LABINFIS), Universidad Nacional de Ingeniería Av. Túpac Amaru 210 Lima Peru
- Centro de Tecnologías de la Información y Comunicaciones (CTIC UNI), Universidad Nacional de Ingenieria Av. Túpac Amaru 210 Lima Peru
| | - Alejandro Lozano
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Unidad Profesional Interdisciplinaria de Biotecnología - Instituto Politécnico Nacional 550 Av. Acueducto 07340 Mexico City Mexico
| | - Harrison B Smith
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo Japan
| | - Jakob Lykke Andersen
- Department of Mathematics and Computer Science, University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Huan Chen
- National High Magnetic Field Laboratory Tallahassee Florida 32310 USA
| | - Markus Meringer
- German Aerospace Center (DLR) 82234 Oberpfaffenhofen Wessling Germany
| | - Henderson James Cleaves
- Blue Marble Space Institute of Science Seattle Washington 98104 USA
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo Japan
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System Chemistry in Catalysis: Facing the Next Challenges in Production of Energy Vectors and Environmental Remediation. Catalysts 2021. [DOI: 10.3390/catal11010064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Most of the catalytic processes that assist the production of either renewable energy vectors or degradation of environmental pollutants rely on the interplay among different factors that can be purposely regulated, in order to improve the overall efficiency of reactions. This perspective analyzes some recent examples of ‘systemic catalysts’, which are based on the modification of the reaction microenvironment and exploitation of concurrent/parasitic reactions or different types of chemical looping, in order to bypass some drawbacks that cannot be easily circumvented by standard approaches. Innovative extensions of those concepts and strategies might inspire new breakthroughs in a variety of key catalytic cycles characterized by high complexity.
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Sawato T, Yamaguchi M. Synthetic Chemical Systems Involving Self‐Catalytic Reactions of Helicene Oligomer Foldamers. Chempluschem 2020; 85:2017-2038. [DOI: 10.1002/cplu.202000489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/18/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Tsukasa Sawato
- Department of Organic Chemistry Graduate School of Pharmaceutical Sciences Tohoku University Aoba Sendai 980-8578 Japan
| | - Masahiko Yamaguchi
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
- Department of Organic Chemistry Graduate School of Pharmaceutical Sciences Tohoku University Aoba Sendai 980-8578 Japan
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Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
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Horváth AK. Law of Mass Action Type Chemical Mechanisms for Modeling Autocatalysis and Hypercycles: Their Role in the Evolutionary Race. Chemphyschem 2020; 21:1703-1710. [PMID: 32367607 PMCID: PMC7496691 DOI: 10.1002/cphc.202000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 01/21/2023]
Abstract
One of our most appealing challenge is to unravel the role of a presumably autocatalytic system in controlling the origin and spreading of Life on our entire planet. Here we show that in the simplest autocatalytic loop involving reactions capable of self-replication and obeying law of mass action kinetics, concentration growth of the autocatalyst may be characterized by parametrization of direct and autocatalytic pathways rather than by kinetic orders of the autocatalyst. Extending this model by feasible elementary steps allows us to outline super-exponential growth where kinetic order of the autocatalyst is higher than unity. Furthermore, it is shown in case of the simplest hypercycle that such a situation might appear where the otherwise more sluggish autocatalytic route receives a decisive support from the crosscatalytic pathway to become an apparently stronger autocatalytic loop even if the other route contains a more efficient autocatalysis. If the hypercycle is performed under flow conditions selection of autocatalyst depends on kinetic and flow parameters influenced by external factors mimicking that the most adaptive loop of hypercycle eventually finds its wining way in the evolutionary race.
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Affiliation(s)
- Attila K. Horváth
- Department of Inorganic ChemistryFaculty of SciencesUniversity of PécsIfjúság u. 6.H-7624PécsHungary
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Sharma K, Wolstenhulme JR, Painter PP, Yeo D, Grande-Carmona F, Johnston CP, Tantillo DJ, Smith MD. Cation-Controlled Enantioselective and Diastereoselective Synthesis of Indolines: An Autoinductive Phase-Transfer Initiated 5-endo-trig Process. J Am Chem Soc 2015; 137:13414-24. [DOI: 10.1021/jacs.5b08834] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Krishna Sharma
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jamie R. Wolstenhulme
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Phillip P. Painter
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - David Yeo
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Francisca Grande-Carmona
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Craig P. Johnston
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Martin D. Smith
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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Bissette AJ, Fletcher SP. Mechanisms of Autocatalysis. Angew Chem Int Ed Engl 2013; 52:12800-26. [DOI: 10.1002/anie.201303822] [Citation(s) in RCA: 273] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Indexed: 12/17/2022]
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Marakushev SA, Belonogova OV. The divergence and natural selection of autocatalytic primordial metabolic systems. ORIGINS LIFE EVOL B 2013; 43:263-81. [PMID: 23860777 DOI: 10.1007/s11084-013-9340-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/28/2013] [Indexed: 11/24/2022]
Abstract
The diversity of the central metabolism of modern organisms is caused by the existence of a few metabolic modules, combination of which produces multiple metabolic pathways. This paper analyzes biomimetically reconstructed coupled autocatalytic cycles as the basis of ancestral metabolic systems. The mechanism for natural selection and evolution in autocatalytic chemical systems may be affected by natural homeostatic parameters such as ambient chemical potentials, temperature, and pressure. Competition between separate parts of an autocatalytic network with positive-plus-negative feedback resulted in the formation of primordial autotrophic, mixotrophic, and heterotrophic metabolic systems. This work examined the last common ancestor of a set of coupled metabolic cycles in a population of protocells. Physical-chemical properties of these cycles determined the main principles of natural selection for the ancestral Bacteria and Archaea taxa.
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Affiliation(s)
- Sergey A Marakushev
- Institute of Problem of Chemical Physics, Russian Academy of Sciences, 142432, Chernogolovka, Moscow Region, Russia.
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12
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Lehn JM. Perspectives in Chemistry-Steps towards Complex Matter. Angew Chem Int Ed Engl 2013; 52:2836-50. [DOI: 10.1002/anie.201208397] [Citation(s) in RCA: 474] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Indexed: 12/16/2022]
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13
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Peters JW, Broderick JB. Emerging paradigms for complex iron-sulfur cofactor assembly and insertion. Annu Rev Biochem 2012; 81:429-50. [PMID: 22482905 DOI: 10.1146/annurev-biochem-052610-094911] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
[FeFe]-hydrogenses and molybdenum (Mo)-nitrogenase are evolutionarily unrelated enzymes with unique complex iron-sulfur cofactors at their active sites. The H cluster of [FeFe]-hydrogenases and the FeMo cofactor of Mo-nitrogenase require specific maturation machinery for their proper synthesis and insertion into the structural enzymes. Recent insights reveal striking similarities in the biosynthetic pathways of these complex cofactors. For both systems, simple iron-sulfur cluster precursors are modified on assembly scaffolds by the activity of radical S-adenosylmethionine (SAM) enzymes. Radical SAM enzymes are responsible for the synthesis and insertion of the unique nonprotein ligands presumed to be key structural determinants for their respective catalytic activities. Maturation culminates in the transfer of the intact cluster assemblies to a cofactor-less structural protein recipient. Required roles for nucleotide binding and hydrolysis have been implicated in both systems, but the specific role for these requirements remain unclear. In this review, we highlight the progress on [FeFe]-hydrogenase H cluster and nitrogenase FeMo-cofactor assembly in the context of these emerging paradigms.
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Affiliation(s)
- John W Peters
- Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana 59717, USA.
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Huber C, Kraus F, Hanzlik M, Eisenreich W, Wächtershäuser G. Elements of metabolic evolution. Chemistry 2012; 18:2063-80. [PMID: 22241585 DOI: 10.1002/chem.201102914] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Indexed: 11/09/2022]
Abstract
Research into the origin of evolution is polarized between a genetics-first approach, with its focus on polymer replication, and a metabolism-first approach that takes aim at chemical reaction cycles. Taking the latter approach, we explored reductive carbon fixation in a volcanic hydrothermal setting, driven by the chemical potential of quenched volcanic fluids for converting volcanic C1 compounds into organic products by transition-metal catalysts. These catalysts are assumed to evolve by accepting ever-new organic products as ligands for enhancing their catalytic power, which in turn enhances the rates of synthetic pathways that give rise to ever-new organic products, with the overall effect of a self-expanding metabolism. We established HCN, CO, and CH(3)SH as carbon nutrients, CO and H(2) as reductants, and iron-group transition metals as catalysts. In one case, we employed the "cyano-system" [Ni(OH)(CN)] with [Ni(CN)(4)](2-) as the dominant nickel-cyano species. This reaction mainly produced α-amino acids and α-hydroxy acids as well as various intermediates and derivatives. An organo-metal-catalyzed mechanism is suggested that mainly builds carbon skeletons by repeated cyano insertions, with minor CO insertions in the presence of CO. The formation of elemental nickel (Ni(0)) points to an active reduced-nickel species. In another case, we employed the mercapto-carbonyl system [Co(2)(CO)(8)]/Ca(OH)(2)/CO for the double-carbonylation of mercaptans. In a "hybrid system", we combined benzyl mercaptan with the cyano system, in which [Ni(OH)(CN)] was the most productive for the double-carbon-fixation reaction. Finally, we demonstrated that the addition of products of the cyano system (Gly, Ala) to the hybrid system increased productivity. These results demonstrate the chemical possibility of metabolic evolution through rate-promotion of one synthetic reaction by the products of another.
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Affiliation(s)
- Claudia Huber
- Lehrstuhl für Biochemie, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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del Amo V, Philp D. Integrating Replication-Based Selection Strategies in Dynamic Covalent Systems. Chemistry 2010; 16:13304-18. [DOI: 10.1002/chem.201000423] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Reznik E, Segrè D. On the stability of metabolic cycles. J Theor Biol 2010; 266:536-49. [PMID: 20673772 DOI: 10.1016/j.jtbi.2010.07.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 04/24/2010] [Accepted: 07/21/2010] [Indexed: 11/18/2022]
Abstract
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of metabolic networks with certain structural regularities can be studied using a combination of analytical and computational techniques. We then apply these techniques to a class of single input, single output metabolic cycles, and find that the cycles are stable under all conditions tested. Next, we extend our analysis to a small autocatalytic cycle, and determine parameter regimes within which the cycle is very likely to be stable. We demonstrate that analytical methods can be used to understand the relationship between kinetic parameters and stability, and that results from these analytical methods can be confirmed with computational experiments. In addition, our results suggest that elevated metabolite concentrations and certain crucial saturation parameters can strongly affect the stability of the entire metabolic cycle. We discuss our results in light of the possibility that evolutionary forces may select for metabolic network topologies with a high intrinsic probability of being stable. Furthermore, our conclusions support the hypothesis that certain types of metabolic cycles may have played a role in the development of primitive metabolism despite the absence of regulatory mechanisms.
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Affiliation(s)
- Ed Reznik
- Bioinformatics Program, 24 Cummington St, Boston, MA, United States. addresses:
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Zotova N, Moran A, Armstrong A, Blackmond D. A Coherent Mechanistic Rationale for Additive Effects and Autoinductive Behaviour in Proline-Mediated Reactions. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200900665] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Eastgate MD, Buono FG. Mechanistic insight into the palladium-catalyzed 1,4-oxidation of 1,3-dienes to 1,4-dicarboxy-alk-2-enes. Angew Chem Int Ed Engl 2009; 48:5958-61. [PMID: 19569150 DOI: 10.1002/anie.200901614] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martin D Eastgate
- Process Research and Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, NJ 08903, USA.
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Busch M, Schlageter M, Weingand D, Gehring T. Systematic studies using 2-(1-adamantylethynyl)pyrimidine-5-carbaldehyde as a starting material in Soai's asymmetric autocatalysis. Chemistry 2009; 15:8251-8. [PMID: 19585641 DOI: 10.1002/chem.200900634] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Herein, we present a new substrate for the Soai reaction, which has an adamantylethynyl residue (1 g) and exhibits asymmetric autocatalysis, yielding products with enantiomeric excesses above 99%. For the first time, all reactions were performed on a parallel synthesizer system to ensure identical reaction conditions. A detailed systematic study of reaction parameters was performed and we report the highest enhancements of enantiomeric excess reported so far in the Soai reaction in one reaction cycle (7.2-->94.1% ee or 3.1-->92.1% ee). Our results led to a set of reaction parameters that yield reproducible results. Therefore, our new starting material 1 g is suitable for systematic and mechanistic studies on this remarkable reaction. A series of experiments designed to quantify the amplification of enantiomeric excess demonstrated that the reaction can be used in principle as a tool for the detection of low enantiomeric excesses: under definite conditions, an unknown low enantiomeric excess (0.1-7%) was amplified to a detectable one. A back calculation to the original value offers a new method for the determination of small enantiomeric excesses.
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Affiliation(s)
- Mark Busch
- Institut für Organische Chemie, Universität Karlsruhe (TH), Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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Eastgate M, Buono F. Mechanistic Insight into the Palladium-Catalyzed 1,4-Oxidation of 1,3-Dienes to 1,4-Dicarboxy-alk-2-enes. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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