1
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Spizzichino S, Di Fonzo F, Marabelli C, Tramonti A, Chaves-Sanjuan A, Parroni A, Boumis G, Liberati FR, Paone A, Montemiglio LC, Ardini M, Jakobi AJ, Bharadwaj A, Swuec P, Tartaglia GG, Paiardini A, Contestabile R, Mai A, Rotili D, Fiorentino F, Macone A, Giorgi A, Tria G, Rinaldo S, Bolognesi M, Giardina G, Cutruzzolà F. Structure-based mechanism of riboregulation of the metabolic enzyme SHMT1. Mol Cell 2024; 84:2682-2697.e6. [PMID: 38996576 DOI: 10.1016/j.molcel.2024.06.016] [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: 04/05/2023] [Revised: 01/26/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
RNA can directly control protein activity in a process called riboregulation; only a few mechanisms of riboregulation have been described in detail, none of which have been characterized on structural grounds. Here, we present a comprehensive structural, functional, and phylogenetic analysis of riboregulation of cytosolic serine hydroxymethyltransferase (SHMT1), the enzyme interconverting serine and glycine in one-carbon metabolism. We have determined the cryoelectron microscopy (cryo-EM) structure of human SHMT1 in its free- and RNA-bound states, and we show that the RNA modulator competes with polyglutamylated folates and acts as an allosteric switch, selectively altering the enzyme's reactivity vs. serine. In addition, we identify the tetrameric assembly and a flap structural motif as key structural elements necessary for binding of RNA to eukaryotic SHMT1. The results presented here suggest that riboregulation may have played a role in evolution of eukaryotic SHMT1 and in compartmentalization of one-carbon metabolism. Our findings provide insights for RNA-based therapeutic strategies targeting this cancer-linked metabolic pathway.
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Affiliation(s)
- Sharon Spizzichino
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Federica Di Fonzo
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Chiara Marabelli
- Department of Molecular Medicine, University of Pavia, Via Forlanini 3, 27100 Pavia, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; Fondazione Romeo e Enrica Invernizzi and NOLIMITS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Alessia Parroni
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Francesca Romana Liberati
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy; Department of Biochemical Sciences, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le A. Moro 5, 00185 Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | - Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience Deft, Delft University of Technology, Van der Maasweg, 92629 HZ Delft, the Netherlands
| | - Alok Bharadwaj
- Department of Bionanoscience, Kavli Institute of Nanoscience Deft, Delft University of Technology, Van der Maasweg, 92629 HZ Delft, the Netherlands
| | - Paolo Swuec
- CryoElectron Microscopy Facility, Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152 Genova, Italy; Department of Biology "Charles Darwin", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Macone
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alessandra Giorgi
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Giancarlo Tria
- CNR Institute of Crystallography - URT Caserta c/o Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; Fondazione Romeo e Enrica Invernizzi and NOLIMITS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy; Department of Biochemical Sciences, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le A. Moro 5, 00185 Rome, Italy.
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2
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Korasick DA, Owuocha LF, Kandoth PK, Tanner JJ, Mitchum MG, Beamer LJ. Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance. FEBS J 2024; 291:323-337. [PMID: 37811683 DOI: 10.1111/febs.16971] [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: 07/17/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Two amino acid variants in soybean serine hydroxymethyltransferase 8 (SHMT8) are associated with resistance to the soybean cyst nematode (SCN), a devastating agricultural pathogen with worldwide economic impacts on soybean production. SHMT8 is a cytoplasmic enzyme that catalyzes the pyridoxal 5-phosphate-dependent conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylenetetrahydrofolate. A previous study of the P130R/N358Y double variant of SHMT8, identified in the SCN-resistant soybean cultivar (cv.) Forrest, showed profound impairment of folate binding affinity and reduced THF-dependent enzyme activity, relative to the highly active SHMT8 in cv. Essex, which is susceptible to SCN. Given the importance of SCN-resistance in soybean agriculture, we report here the biochemical and structural characterization of the P130R and N358Y single variants to elucidate their individual effects on soybean SHMT8. We find that both single variants have reduced THF-dependent catalytic activity relative to Essex SHMT8 (10- to 50-fold decrease in kcat /Km ) but are significantly more active than the P130R/N368Y double variant. The kinetic data also show that the single variants lack THF-substrate inhibition as found in Essex SHMT8, an observation with implications for regulation of the folate cycle. Five crystal structures of the P130R and N358Y variants in complex with various ligands (resolutions from 1.49 to 2.30 Å) reveal distinct structural impacts of the mutations and provide new insights into allosterism. Our results support the notion that the P130R/N358Y double variant in Forrest SHMT8 produces unique and unexpected effects on the enzyme, which cannot be easily predicted from the behavior of the individual variants.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Luckio F Owuocha
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Pramod K Kandoth
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Melissa G Mitchum
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Plant Pathology, Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, USA
| | - Lesa J Beamer
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
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3
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Maenpuen S, Mee-Udorn P, Pinthong C, Athipornchai A, Phiwkaow K, Watchasit S, Pimviriyakul P, Rungrotmongkol T, Tinikul R, Leartsakulpanich U, Chitnumsub P. Mangiferin is a new potential antimalarial and anticancer drug for targeting serine hydroxymethyltransferase. Arch Biochem Biophys 2023; 745:109712. [PMID: 37543353 DOI: 10.1016/j.abb.2023.109712] [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: 06/30/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
Mangiferin, a polyphenolic xanthone glycoside found in various botanical sources, including mango (Mangifera indica L.) leaves, can exhibit a variety of bioactivities. Although mangiferin has been reported to inhibit many targets, none of the studies have investigated the inhibition of serine hydroxymethyltransferase (SHMT), an attractive target for antimalarial and anticancer drugs. SHMT, one of the key enzymes in the deoxythymidylate synthesis cycle, catalyzes the reversible conversion of l-serine and (6S)-tetrahydrofolate (THF) into glycine and 5,10-methylene THF. Here, in vitro and in silico studies were used to probe how mangiferin isolated from mango leaves inhibits Plasmodium falciparum and human cytosolic SHMTs. The inhibition kinetics at pH 7.5 revealed that mangiferin is a competitive inhibitor against THF for enzymes from both organisms. Molecular docking and molecular dynamic (MD) simulations demonstrated the inhibitory effects of the deprotonated forms of mangiferin, specifically the C6-O- species and its resonance C9-O- species appearing at pH 7.5, combined with two docked poses, either a xanthone or glucose moiety, placed inside the THF-binding pocket. The MD analysis revealed that both C6-O- and its resonance-stabilized C9-O- species can favorably bind to SHMT in a similar fashion to THF, supporting the THF competitive inhibition of mangiferin. In addition, characterization of the proton dissociation equilibria of isolated mangiferin revealed that only three hydroxy groups of the xanthone moiety, C6-OH, C3-OH, and C7-OH, underwent varying degrees of deprotonation with pKa values of 6.38 ± 0.11, 8.21 ± 0.35, and 12.37 ± 0.30, respectively, while C1-OH remained protonated. Altogether, our findings demonstrate a new bioactivity of mangiferin and provide the basis for the future development of mangiferin as a potent antimalarial and anticancer drug.
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Affiliation(s)
- Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand.
| | - Pitchayathida Mee-Udorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chatchadaporn Pinthong
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Anan Athipornchai
- The Research Unit in Synthetic Compounds and Synthetic Analogues from Natural Product for Drug Discovery, Center of Excellence for Innovation in Chemistry and Department of Chemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand
| | - Kochakorn Phiwkaow
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand
| | - Sarayut Watchasit
- Nuclear Magnetic Resonance Spectroscopic Laboratory, Science Innovation Facility, Faculty of Science, Burapha University, Chonburi, 20131, Thailand
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
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4
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Shamshad H, Bakri R, Mirza AZ. Dihydrofolate reductase, thymidylate synthase, and serine hydroxy methyltransferase: successful targets against some infectious diseases. Mol Biol Rep 2022; 49:6659-6691. [PMID: 35253073 PMCID: PMC8898753 DOI: 10.1007/s11033-022-07266-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Parasitic diseases have a serious impact on the world in terms of health and economics and are responsible for worldwide mortality and morbidity. The present review features the hybrid targeting involving three main enzymes for the treatment of different parasitic diseases. The enzymes Dihydrofolate reductase, thymidylate synthase, and Serine hydroxy methyltransferase play an essential role in the folate pathway. The present review focuses on these enzymes, which can be targeted against several diseases. It shed light on the past, present, and future of these targets, and it can be assessed that these targets can play a significant role against several infectious diseases. For combating viral and protozoal infectious diseases, these targets in combination should be addressed.
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Affiliation(s)
- Hina Shamshad
- Faculty of Pharmacy, Jinnah University for Women, Karachi, Pakistan
| | - Rowaida Bakri
- College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
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5
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Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance. Int J Biol Macromol 2020; 159:517-529. [PMID: 32417544 DOI: 10.1016/j.ijbiomac.2020.05.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal 5'-phosphate-dependent enzyme that plays a pivotal role in cellular one‑carbon metabolism. In plants and cyanobacteria, this enzyme is also involved in photorespiration and confers salt tolerance, as in the case of SHMT from the halophilic cyanobacterium Aphanothece halophytica (AhSHMT). We have characterized the catalytic properties of AhSHMT in different salt and pH conditions. Although the kinetic properties of AhSHMT correlate with those of the mesophilic orthologue from Escherichia coli, AhSHMT appears more catalytically efficient, especially in presence of salt. Our studies also reveal substrate inhibition, previously unobserved in AhSHMT. Furthermore, addition of the osmoprotectant glycine betaine under salt conditions has a distinct positive effect on AhSHMT activity. The crystal structures of AhSHMT in three forms, as internal aldimine, as external aldimine with the l-serine substrate, and as a covalent complex with malonate, give structural insights on the possible role of specific amino acid residues implicated in the halophilic features of AhSHMT. Importantly, we observed that overexpression of the gene encoding SHMT, independently from its origin, increases the capability of E. coli to grow in high salt conditions, suggesting that the catalytic activity of this enzyme in itself plays a fundamental role in salt tolerance.
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6
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Ruszkowski M, Sekula B, Ruszkowska A, Contestabile R, Nogues I, Angelaccio S, Szczepaniak A, Dauter Z. Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models. Sci Rep 2019; 9:19614. [PMID: 31873125 PMCID: PMC6928210 DOI: 10.1038/s41598-019-56043-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/05/2019] [Indexed: 12/19/2022] Open
Abstract
Serine hydroxymethyltransferases (SHMTs) reversibly transform serine into glycine in a reaction accompanied with conversion of tetrahydrofolate (THF) into 5,10-methylene-THF (5,10-meTHF). In vivo, 5,10-meTHF is the main carrier of one-carbon (1C) units, which are utilized for nucleotide biosynthesis and other processes crucial for every living cell, but hyperactivated in overproliferating cells (e.g. cancer tissues). SHMTs are emerging as a promising target for development of new drugs because it appears possible to inhibit growth of cancer cells by cutting off the supply of 5,10-meTHF. Methotrexate (MTX) and pemetrexed (PTX) are two examples of antifolates that have cured many patients over the years but target different enzymes from the folate cycle (mainly dihydrofolate reductase and thymidylate synthase, respectively). Here we show crystal structures of MTX and PTX bound to plant SHMT isozymes from cytosol and mitochondria-human isozymes exist in the same subcellular compartments. We verify inhibition of the studied isozymes by a thorough kinetic analysis. We propose to further exploit antifolate scaffold in development of SHMT inhibitors because it seems likely that especially polyglutamylated PTX inhibits SHMTs in vivo. Structure-based optimization is expected to yield novel antifolates that could potentially be used as chemotherapeutics.
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Affiliation(s)
- Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA.
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Bartosz Sekula
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Roberto Contestabile
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Roma, Italy
| | - Isabel Nogues
- Research Institute of Terrestrial Ecosystems, Italian National Research Council, Via Salaria Km. 29, 300-00015, Monterotondo Scalo, Roma, Italy
| | - Sebastiana Angelaccio
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Roma, Italy
| | - Andrzej Szczepaniak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA
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7
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Guiducci G, Paone A, Tramonti A, Giardina G, Rinaldo S, Bouzidi A, Magnifico MC, Marani M, Menendez JA, Fatica A, Macone A, Armaos A, Tartaglia GG, Contestabile R, Paiardini A, Cutruzzolà F. The moonlighting RNA-binding activity of cytosolic serine hydroxymethyltransferase contributes to control compartmentalization of serine metabolism. Nucleic Acids Res 2019; 47:4240-4254. [PMID: 30809670 PMCID: PMC6486632 DOI: 10.1093/nar/gkz129] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/01/2019] [Accepted: 02/15/2019] [Indexed: 12/30/2022] Open
Abstract
Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential for the one-carbon metabolism, which sustains growth and proliferation in normal and tumour cells. Here, we characterize the RNA-binding function of cytosolic SHMT (SHMT1) in vitro and using cancer cell models. We show that SHMT1 controls the expression of its mitochondrial counterpart (SHMT2) by binding to the 5'untranslated region of the SHMT2 transcript (UTR2). Importantly, binding to RNA is modulated by metabolites in vitro and the formation of the SHMT1-UTR2 complex inhibits the serine cleavage activity of the SHMT1, without affecting the reverse reaction. Transfection of UTR2 in cancer cells controls SHMT1 activity and reduces cell viability. We propose a novel mechanism of SHMT regulation, which interconnects RNA and metabolites levels to control the cross-talk between cytosolic and mitochondrial compartments of serine metabolism.
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Affiliation(s)
- Giulia Guiducci
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Angela Tramonti
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Amani Bouzidi
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Maria C Magnifico
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Marina Marani
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, 17007 Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, 00185 Rome, Italy
| | - Alberto Macone
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Gian G Tartaglia
- Department of Biology and Biotechnology 'C. Darwin', Sapienza University of Rome, 00185 Rome, Italy.,Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, 08003 Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Department of Life and Medical Sciences, 23 Passeig Lluıs Companys, 08010 Barcelona, Spain
| | - Roberto Contestabile
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome - P. le Aldo Moro 5, 00185 Rome, Italy
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8
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Ubonprasert S, Jaroensuk J, Pornthanakasem W, Kamonsutthipaijit N, Wongpituk P, Mee-Udorn P, Rungrotmongkol T, Ketchart O, Chitnumsub P, Leartsakulpanich U, Chaiyen P, Maenpuen S. A flap motif in human serine hydroxymethyltransferase is important for structural stabilization, ligand binding, and control of product release. J Biol Chem 2019; 294:10490-10502. [PMID: 31118236 DOI: 10.1074/jbc.ra119.007454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible "flap motif" whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6S)-tetrahydrofolate (THF)-dependent reactions compared with the WT but had similar activity in THF-independent aldol cleavage of β-hydroxyamino acid. hcSHMT/Δflap was less sensitive to THF inhibition than the WT (Ki of 0.65 and 0.27 mm THF at pH 7.5, respectively), and the THF dissociation constant of the WT was also 3-fold lower than that of hcSHMT/Δflap, indicating that the flap is important for THF binding. hcSHMT/Δflap did not display the burst kinetics observed in the WT. These results indicate that, upon removal of the flap, product release is no longer the rate-limiting step, implying that the flap is important for controlling product release. The findings reported here improve our understanding of the functional roles of the flap motif in hcSHMT and provide fundamental insight into how a flexible loop can be involved in controlling the enzymatic reactions of hcSHMT and other enzymes.
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Affiliation(s)
- Sakunrat Ubonprasert
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Wichai Pornthanakasem
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | | | - Peerapong Wongpituk
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, and
| | - Pitchayathida Mee-Udorn
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and
| | - Thanyada Rungrotmongkol
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and.,Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, and
| | - Onuma Ketchart
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | - Ubolsree Leartsakulpanich
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and
| | - Pimchai Chaiyen
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.,School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
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9
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Santatiwongchai J, Gleeson D, Gleeson MP. Theoretical Evaluation of the Reaction Mechanism of Serine Hydroxymethyltransferase. J Phys Chem B 2019; 123:407-418. [PMID: 30522268 DOI: 10.1021/acs.jpcb.8b10196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene THF. SHMT is a folate pathway enzyme and is therefore of considerable medical interest due to its role as an important intervention point for antimalarial, anticancer, and antibacterial treatments. Despite considerable experimental effort, the precise reaction mechanism of SHMT remains unclear. In this study, we explore the mechanism of SHMT to determine the roles of active site residues and the nature and the sequence of chemical steps. Molecular dynamics (MD) methods were employed to generate a suitable starting structure which then underwent analysis using hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. The QM region consisted of 12 key residues, two substrates, and explicit solvent. Our results show that the catalytic reaction proceeds according to a retro-aldol synthetic process with His129 acting as the general base in the reaction. The rate-determining step involves the cleavage of the PLP-serine aldimine Cα-Cβ bond and the formation of formaldehyde in line with experimental evidence. The pyridyl ring of the PLP-serine aldimine substrate exists in deprotonated form, being stabilized directly by Asp208 via a strong H-bond, as well as through interactions with Arg371, Lys237, and His211, and with the surrounding protein which was electrostatically embedded. This knowledge has the potential to impact the design and development of new inhibitors.
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Affiliation(s)
- Jirapat Santatiwongchai
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
| | - Duangkamol Gleeson
- Department of Chemistry, Faculty of Science , King Mongkut's Institute of Technology Ladkrabang , Bangkok 10520 , Thailand
| | - M Paul Gleeson
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand.,Department of Biomedical Engineering, Faculty of Engineering , King Mongkut's Institute of Technology Ladkrabang , Bangkok 10520 , Thailand
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10
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Tramonti A, Nardella C, di Salvo ML, Barile A, Cutruzzolà F, Contestabile R. Human Cytosolic and Mitochondrial Serine Hydroxymethyltransferase Isoforms in Comparison: Full Kinetic Characterization and Substrate Inhibition Properties. Biochemistry 2018; 57:6984-6996. [PMID: 30500180 DOI: 10.1021/acs.biochem.8b01074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Serine hydroxymethyltransferase (SHMT) catalyzes the reversible conversion of l-serine and tetrahydrofolate into glycine and 5,10-methylenetetrahydrofolate. This enzyme, which plays a pivotal role in one-carbon metabolism, is involved in cancer metabolic reprogramming and is a recognized target of chemotherapy intervention. In humans, two isoforms of the enzyme exist, which are commonly termed cytosolic SHMT1 and mitochondrial SHMT2. Considerable attention has been paid to the structural, mechanistic, and metabolic features of these isozymes. On the other hand, a detailed comparison of their catalytic and regulatory properties is missing, although this aspect seems to be considerably important, considering that SHMT1 and SHMT2 reside in different cellular compartments, where they play distinct roles in folate metabolism. Here we performed a full kinetic characterization of the serine hydroxymethyltransferase reaction catalyzed by SHMT1 and SHMT2, with a focus on pH dependence and substrate inhibition. Our investigation, which allowed the determination of all kinetic parameters of serine hydroxymethyltransferase forward and backward reactions, uncovered a previously unobserved substrate inhibition by l-serine and highlighted several interesting differences between SHMT1 and SHMT2. In particular, SHMT2 maintains a pronounced tetrahydrofolate substrate inhibition even at the alkaline pH characteristic of the mitochondrial matrix, whereas with SHMT1 this is almost abolished. At this pH, SHMT2 also shows a catalytic efficiency that is much higher than that of SHMT1. These observations suggest that such different properties represent an adaptation of the isoforms to the respective cellular environments and that substrate inhibition may be a form of regulation.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari , Consiglio Nazionale delle Ricerche , Piazzale Aldo Moro 5 , 00185 Roma , Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" , Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti , Piazzale Aldo Moro 5 , 00185 Roma , Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" , Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti , Piazzale Aldo Moro 5 , 00185 Roma , Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" , Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti , Piazzale Aldo Moro 5 , 00185 Roma , Italy
| | - Anna Barile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" , Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti , Piazzale Aldo Moro 5 , 00185 Roma , Italy
| | - Francesca Cutruzzolà
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" , Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti , Piazzale Aldo Moro 5 , 00185 Roma , Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" , Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti , Piazzale Aldo Moro 5 , 00185 Roma , Italy
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11
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Zhou K, Ding X, Yang J, Hu Y, Song Y, Chen M, Sun R, Dong T, Xu B, Han X, Wu K, Zhang X, Wang X, Xia Y. Metabolomics Reveals Metabolic Changes Caused by Low-Dose 4-Tert-Octylphenol in Mice Liver. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15122686. [PMID: 30487447 PMCID: PMC6313621 DOI: 10.3390/ijerph15122686] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/19/2018] [Accepted: 11/25/2018] [Indexed: 01/16/2023]
Abstract
Background: Humans are constantly exposed to low concentrations of 4-tert-octylphenol (OP). However, studies investigating the effects of low-dose OP on the liver are scarce, and the mechanism of these effects has not been thoroughly elucidated to date. Methods: Adult male institute of cancer research (ICR) mice were exposed to low-dose OP (0, 0.01 and 1 μg/kg/day) for 7 consecutive days. Weights of mice were recorded daily during the experiment. Blood serum levels of OP, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were determined, and haematoxylin-eosin (HE) staining of the liver was performed. We applied an integrated metabolomic and enzyme gene expression analysis to investigate liver metabolic changes, and the gene expression of related metabolic enzymes was determined by real-time PCR and ELISA. Results: OP in blood serum was increased after OP exposure, while body weights of mice were unchanged. Liver weight and its organ coefficient were decreased significantly in the OP (1 μg/kg/day) group, but ALT and AST, as well as the HE staining results, were unchanged after OP treatment. The levels of cytidine, uridine, purine and N-acetylglutamine were increased significantly, and the level of vitamin B6 was decreased significantly in mice treated with OP (1 μg/kg/day). The mRNA and protein levels of Cda and Shmt1 were both increased significantly in OP (1 μg/kg/day)-treated mice. Conclusions: Through metabolomic analysis, our study firstly found that pyrimidine and purine synthesis were promoted and that N-acetylglutamine was upregulated after low-dose OP treatment, indicating that the treatment disturbed nucleic acid and amino acid metabolism in mice liver.
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Affiliation(s)
- Kun Zhou
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Xingwang Ding
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Jing Yang
- Experiment Center for Teaching and Learning, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Yanhui Hu
- Safety Assessment and Research Center for Drug, Pesticide, and Veterinary Drug of Jiangsu Province, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Yun Song
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Tianyu Dong
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Bo Xu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Xiumei Han
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Keqin Wu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Xiaoling Zhang
- Department of Hygienic Analysis and Detection, Nanjing Medical University, Nanjing 211166, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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12
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Méhul B, Perrin A, Grisendi K, Galindo AN, Dayon L, Ménigot C, Rival Y, Voegel JJ. Mass spectrometry and DigiWest technology emphasize protein acetylation profile from Quisinostat-treated HuT78 CTCL cell line. J Proteomics 2018; 187:126-143. [PMID: 30012418 DOI: 10.1016/j.jprot.2018.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/20/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023]
Abstract
Histone deacetylases (HDACs) are key enzymes involved in epigenetic modulation and were targeted by HDAC inhibitors (HDACis) for cancer treatment. The action of HDACis is not restricted to histones and also prevents deacetylation of other proteins, supporting their wide biological actions. The HuT78 cell line is recognized as a key tool to support and understand cutaneous T-cell lymphoma (CTCL) biology and was used as a predictive model since HDACi such as Vorinostat and Panobinostat have both demonstrated apoptotic activities in HuT78 cells and in primary blood CTCL cells. In this study, Quisinostat (JNJ-26481585) a novel second-generation HDACi with highest potency for HDAC1, was tested on HuT78 cell line. Quantitative mass spectrometry (MS)-based proteomics after acetylated-lysine peptide enrichment and a targeted antibody-based immunoassay (DigiWest) were used as complementary technologies to assess the modifications of the acetylated proteome. As expected, several acetylated lysines of histones were increased by the HDACi. Additional acetylated non-histone proteins were modulated after treatment with Quisinostat including the nucleolin (a major nucleolar protein), the replication protein A 70 kDa DNA-binding subunit, the phosphoglycerate kinase 1, the stress-70 protein, the proto-oncogene Myc and the serine hydroxymethyltransferase. A better knowledge of histone and non-histone acetylated protein profile after Quisinostat treatment can strongly support the understanding of non-clinical and clinical results of this HDACi. These technological tools can also help in designing new HDACis in a pharmaceutical drug discovery program. SIGNIFICANCE A better knowledge of histone and non-histone acetylated protein profile after HDAC inhibitors (HDACis) treatment can strongly support the understanding of non-clinical and clinical investigations in a pharmaceutical drug discovery program. Relative quantification using mass spectrometry -based proteomics after acetylated-lysine peptide enrichment and a targeted antibody-based immunoassay (DigiWest) are proposed as complementary technologies to assess the modifications of the acetylated proteome. Quisinostat (JNJ-26481585) a novel second-generation HDACi with highest potency for HDAC1 was better characterized in vitro in HuT78 cells to support and understand cutaneous T-cell lymphoma (CTCL) therapeutic research program.
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Affiliation(s)
- Bruno Méhul
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France.
| | - Agnes Perrin
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | - Karine Grisendi
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | | | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Corinne Ménigot
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | - Yves Rival
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
| | - Johannes J Voegel
- Galderma, Nestlé Skin Health R & D, 2400, route des Colles, 06410 Biot, France
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13
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Tramonti A, Paiardini A, Paone A, Bouzidi A, Giardina G, Guiducci G, Magnifico MC, Rinaldo S, McDermott L, Menendez JA, Contestabile R, Cutruzzolà F. Differential inhibitory effect of a pyrazolopyran compound on human serine hydroxymethyltransferase-amino acid complexes. Arch Biochem Biophys 2018; 653:71-79. [PMID: 29991441 DOI: 10.1016/j.abb.2018.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/05/2018] [Accepted: 07/02/2018] [Indexed: 12/14/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a pivotal enzyme in one-carbon metabolism that catalyses the reversible conversion of serine and tetrahydrofolate into glycine and methylenetetrahydrofolate. It exists in cytosolic (SHMT1) and mitochondrial (SHMT2) isoforms. Research on one-carbon metabolism in cancer cell lines has shown that SHMT1 preferentially catalyses serine synthesis, whereas in mitochondria SHMT2 is involved in serine breakdown. Recent research has focused on the identification of inhibitors that bind at the folate pocket. We have previously found that a representative derivative of the pyrazolopyran scaffold, namely 2.12, inhibits both SHMT isoforms, with a preference for SHMT1, causing apoptosis in lung cancer cell lines. Here we show that the affinity of 2.12 for SHMT depends on the identity of the amino acid substrate bound to the enzyme. The dissociation constant of 2.12 is 50-fold lower when it binds to SHMT1 enzyme-serine complex, as compared to the enzyme-glycine complex. Evidence is presented for a similar behaviour of compound 2.12 in the cellular environment. These findings suggest that the presence and identity of the amino acid substrate should be considered when designing SHMT inhibitors. Moreover, our data provide the proof-of-concept that SHMT inhibitors selectively targeting the directionality of one-carbon metabolism flux could be designed.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro 5, 00185, Roma, Italy; Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Alessandro Paiardini
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Alessio Paone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Amani Bouzidi
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Giorgio Giardina
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Giulia Guiducci
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Maria Chiara Magnifico
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Serena Rinaldo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Lee McDermott
- Department of Pharmaceutical Sciences and Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Catalonia, Spain; Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy.
| | - Francesca Cutruzzolà
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy.
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