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Coutinho LP, Silva SRB, de Lima-Neto P, Monteiro NDKV. A mechanistic insight for the biosynthesis of N,N-dimethyltryptamine: An ONIOM theoretical approach. Biochem Biophys Res Commun 2023; 678:148-157. [PMID: 37640000 DOI: 10.1016/j.bbrc.2023.08.043] [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: 06/09/2023] [Revised: 07/31/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
Psychoactive natural products are potent serotonergic agonists capable of modulating brain functions such as memory and cognition. These substances have shown therapeutic potential for treating various mental disorders. The fact that N,N-dimethyltryptamine (DMT) is produced endogenously in several plants and animals, including humans, makes it particularly attractive. As an amino acid-derived alkaloid, the DMT biosynthetic pathway is part of the L-tryptophan biochemical cascade and can be divided into the decarboxylation by an aromatic L-amino acid decarboxylase (AADC) for tryptamine formation and the subsequent double-methylation by the indolethylamine-N-methyltransferase (INMT) through the cofactor S-adenosyl-L-methionine (SAM), a methyl donor. Unlike the decarboxylation mechanism of L-tryptophan, the molecular details of the double methylation of tryptamine have not been elucidated. Therefore, we propose an in silico model using molecular dynamics (MD), non-covalent interaction index (NCI) and density functional theory (DFT) calculations with the ONIOM QM:MM B3LYP/6-31+G(d,p):MM/UFF level of theory. Based on the obtained energetic data, the potential energy surface (PES) indicates an SN2 mechanism profile, with the second methylation energy barrier being the rate-limiting step with δG‡=60kJ∙mol-1 larger than the previous methylation, following the NCI analysis showing more repulsive interactions for the second transition state. In addition, the hybridization information of each reaction step provides geometric details about the double-methylation.
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Affiliation(s)
- Lucas Pinheiro Coutinho
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, 60021-970, Fortaleza, CE, Brazil
| | | | - Pedro de Lima-Neto
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, 60021-970, Fortaleza, CE, Brazil
| | - Norberto de Kássio Vieira Monteiro
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, 60021-970, Fortaleza, CE, Brazil.
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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Mee-udorn P, Nutho B, Chootrakool R, Maenpuen S, Leartsakulpanich U, Chitnumsub P, Rungrotmongkol T. Structural dynamics and in silico design of pyrazolopyran-based inhibitors against Plasmodium serine hydroxymethyltransferases. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Maity AN, Chen JR, Li QY, Ke SC. The Nitrogen Atom of Vitamin B 6 Is Essential for the Catalysis of Radical Aminomutases. Int J Mol Sci 2022; 23:ijms23095210. [PMID: 35563602 PMCID: PMC9105233 DOI: 10.3390/ijms23095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B6 vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.
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Monti M, Guiducci G, Paone A, Rinaldo S, Giardina G, Liberati FR, Cutruzzolá F, Tartaglia GG. Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments. Comput Struct Biotechnol J 2021; 19:3034-3041. [PMID: 34136101 PMCID: PMC8175283 DOI: 10.1016/j.csbj.2021.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 01/15/2023] Open
Abstract
Human serine hydroxymethyltransferase (SHMT) regulates the serine-glycine one carbon metabolism and plays a role in cancer metabolic reprogramming. Two SHMT isozymes are acting in the cell: SHMT1 encoding the cytoplasmic isozyme, and SHMT2 encoding the mitochondrial one. Here we present a molecular model built on experimental data reporting the interaction between SHMT1 protein and SHMT2 mRNA, recently discovered in lung cancer cells. Using a stochastic dynamic model, we show that RNA moieties dynamically regulate serine and glycine concentration, shaping the system behaviour. For the first time we observe an active functional role of the RNA in the regulation of the serine-glycine metabolism and availability, which unravels a complex layer of regulation that cancer cells exploit to fine tune amino acids availability according to their metabolic needs. The quantitative model, complemented by an experimental validation in the lung adenocarcinoma cell line H1299, exploits RNA molecules as metabolic switches of the SHMT1 activity. Our results pave the way for the development of RNA-based molecules able to unbalance serine metabolism in cancer cells.
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Affiliation(s)
- Michele Monti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- RNA System Biology Lab, Centre for Human Technologies, Istituto Italiano di Tecnologia (IIT), Enrico Melen 83, 16152 Genova, Italy
| | - Giulia Guiducci
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Francesca Romana Liberati
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Francesca Cutruzzolá
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- RNA System Biology Lab, Centre for Human Technologies, Istituto Italiano di Tecnologia (IIT), Enrico Melen 83, 16152 Genova, Italy
- ICREA, Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
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