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E Costa RK, Rodrigues CT, H Campos JC, Paradela LS, Dias MM, Novaes da Silva B, de Valega Negrao CVZ, Gonçalves KDA, Ascenção CFR, Adamoski D, Mercaldi GF, Bastos ACS, Batista FAH, Figueira AC, Cordeiro AT, Ambrosio ALB, Guido RVC, Dias SMG. High-Throughput Screening Reveals New Glutaminase Inhibitor Molecules. ACS Pharmacol Transl Sci 2021; 4:1849-1866. [PMID: 34927015 DOI: 10.1021/acsptsci.1c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 11/29/2022]
Abstract
The glutaminase (GLS) enzyme hydrolyzes glutamine into glutamate, an important anaplerotic source for the tricarboxylic acid cycle in rapidly growing cancer cells under the Warburg effect. Glutamine-derived α-ketoglutarate is also an important cofactor of chromatin-modifying enzymes, and through epigenetic changes, it keeps cancer cells in an undifferentiated state. Moreover, glutamate is an important neurotransmitter, and deregulated glutaminase activity in the nervous system underlies several neurological disorders. Given the proven importance of glutaminase for critical diseases, we describe the development of a new coupled enzyme-based fluorescent glutaminase activity assay formatted for 384-well plates for high-throughput screening (HTS) of glutaminase inhibitors. We applied the new methodology to screen a ∼30,000-compound library to search for GLS inhibitors. The HTS assay identified 11 glutaminase inhibitors as hits that were characterized by in silico, biochemical, and glutaminase-based cellular assays. A structure-activity relationship study on the most promising hit (C9) allowed the discovery of a derivative, C9.22, with enhanced in vitro and cellular glutaminase-inhibiting activity. In summary, we discovered a new glutaminase inhibitor with an innovative structural scaffold and described the molecular determinants of its activity.
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Affiliation(s)
- Renna K E Costa
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas-UNICAMP, 13083-970 Campinas-SP, Brazil
| | - Camila T Rodrigues
- Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), 13563-120 Sao Carlos-SP, Brazil
| | - Jean C H Campos
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Luciana S Paradela
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas-UNICAMP, 13083-970 Campinas-SP, Brazil
| | - Marilia M Dias
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Bianca Novaes da Silva
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Cyro von Zuben de Valega Negrao
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas-UNICAMP, 13083-970 Campinas-SP, Brazil
| | - Kaliandra de Almeida Gonçalves
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Carolline F R Ascenção
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas-UNICAMP, 13083-970 Campinas-SP, Brazil
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas-UNICAMP, 13083-970 Campinas-SP, Brazil
| | - Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Alliny C S Bastos
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Fernanda A H Batista
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Ana Carolina Figueira
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Artur T Cordeiro
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Andre L B Ambrosio
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
| | - Rafael V C Guido
- Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), 13563-120 Sao Carlos-SP, Brazil
| | - Sandra M G Dias
- Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-100 Campinas-SP, Brazil
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Mercaldi GF, Andrade MDO, Zanella JDL, Cordeiro AT, Benedetti CE. Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium. J Biol Chem 2021; 296:100658. [PMID: 33857480 PMCID: PMC8165550 DOI: 10.1016/j.jbc.2021.100658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
Gram-negative bacteria are responsible for a variety of human, animal, and plant diseases. The spread of multidrug-resistant Gram-negative bacteria poses a challenge to disease control and highlights the need for novel antimicrobials. Owing to their critical role in protein synthesis, aminoacyl-tRNA synthetases, including the methionyl-tRNA synthetases MetRS1 and MetRS2, are attractive drug targets. MetRS1 has long been exploited as a drug target in Gram-positive bacteria and protozoan parasites. However, MetRS1 inhibitors have limited action upon Gram-negative pathogens or on Gram-positive bacteria that produce MetRS2 enzymes. The underlying mechanism by which MetRS2 enzymes are insensitive to MetRS1 inhibitors is presently unknown. Herein, we report the first structures of MetRS2 from a multidrug-resistant Gram-negative bacterium in its ligand-free state and bound to its substrate or MetRS1 inhibitors. The structures reveal the binding mode of two diaryldiamine MetRS1 inhibitors that occupy the amino acid-binding site and a surrounding auxiliary pocket implicated in tRNA acceptor arm binding. The structural features associated with amino acid polymorphisms found in the methionine and auxiliary pockets reveal the molecular basis for diaryldiamine binding and selectivity between MetRS1 and MetRS2 enzymes. Moreover, we show that mutations in key polymorphic residues in the methionine and auxiliary pockets not only altered inhibitor binding affinity but also significantly reduced enzyme function. Our findings thus reinforce the tRNA acceptor arm binding site as a druggable pocket in class I aminoacyl-tRNA synthetases and provide a structural basis for optimization of MetRS2 inhibitors for the development of new antimicrobials against Gram-negative pathogens.
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Affiliation(s)
- Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.
| | - Maxuel de Oliveira Andrade
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Jackeline de Lima Zanella
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Artur Torres Cordeiro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.
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Shimo HM, Terassi C, Lima Silva CC, Zanella JDL, Mercaldi GF, Rocco SA, Benedetti CE. Role of the Citrus sinensis RNA deadenylase CsCAF1 in citrus canker resistance. Mol Plant Pathol 2019; 20:1105-1118. [PMID: 31115151 PMCID: PMC6640180 DOI: 10.1111/mpp.12815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Poly(A) tail shortening is a critical step in messenger RNA (mRNA) decay and control of gene expression. The carbon catabolite repressor 4 (CCR4)-associated factor 1 (CAF1) component of the CCR4-NOT deadenylase complex plays an essential role in mRNA deadenylation in most eukaryotes. However, while CAF1 has been extensively investigated in yeast and animals, its role in plants remains largely unknown. Here, we show that the Citrus sinensis CAF1 (CsCAF1) is a magnesium-dependent deadenylase implicated in resistance against the citrus canker bacteria Xanthomonas citri. CsCAF1 interacted with proteins of the CCR4-NOT complex, including CsVIP2, a NOT2 homologue, translin-associated factor X (CsTRAX) and the poly(A)-binding proteins CsPABPN and CsPABPC. CsCAF1 also interacted with PthA4, the main X. citri effector required for citrus canker elicitation. We also present evidence suggesting that PthA4 inhibits CsCAF1 deadenylase activity in vitro and stabilizes the mRNA encoded by the citrus canker susceptibility gene CsLOB1, which is transcriptionally activated by PthA4 during canker formation. Moreover, we show that an inhibitor of CsCAF1 deadenylase activity significantly enhanced canker development, despite causing a reduction in PthA4-dependent CsLOB1 transcription. These results thus link CsCAF1 with canker development and PthA4-dependent transcription in citrus plants.
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Affiliation(s)
- Hugo Massayoshi Shimo
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Carolina Terassi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Caio Cesar Lima Silva
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Jackeline de Lima Zanella
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Silvana Aparecida Rocco
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
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Lima Silva CCD, Shimo HM, de Felício R, Mercaldi GF, Rocco SA, Benedetti CE. Structure-function relationship of a citrus salicylate methylesterase and role of salicylic acid in citrus canker resistance. Sci Rep 2019; 9:3901. [PMID: 30846791 PMCID: PMC6405950 DOI: 10.1038/s41598-019-40552-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/18/2019] [Indexed: 11/09/2022] Open
Abstract
Salicylic acid (SA) and its methyl ester, methyl salicylate (MeSA) are well known inducers of local and systemic plant defense responses, respectively. MeSA is a major mediator of systemic acquired resistance (SAR) and its conversion back into SA is thought to be required for SAR. In many plant species, conversion of MeSA into SA is mediated by MeSA esterases of the SABP2 family. Here we show that the Citrus sinensis SABP2 homologue protein CsMES1 catalyzes the hydrolysis of MeSA into SA. Molecular modeling studies suggest that CsMES1 shares the same structure and SA-binding mode with tobacco SABP2. However, an amino acid polymorphism in the active site of CsMES1-related proteins suggested an important role in enzyme regulation. We present evidence that the side chain of this polymorphic residue directly influences enzyme activity and SA binding affinity in CsMES proteins. We also show that SA and CsMES1 transcripts preferentially accumulate during the incompatible interaction between Xanthomonas aurantifolii pathotype C and sweet orange plants. Moreover, we demonstrate that SA and MeSA inhibited citrus canker caused by Xanthomonas citri, whereas an inhibitor of CsMES1 enhanced canker formation, suggesting that CsMES1 and SA play a role in the local defense against citrus canker bacteria.
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Affiliation(s)
- Caio Cesar de Lima Silva
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP, 13083-100, Campinas, SP, Brazil
| | - Hugo Massayoshi Shimo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP, 13083-100, Campinas, SP, Brazil
| | - Rafael de Felício
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP, 13083-100, Campinas, SP, Brazil
| | - Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP, 13083-100, Campinas, SP, Brazil
| | - Silvana Aparecida Rocco
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP, 13083-100, Campinas, SP, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), CEP, 13083-100, Campinas, SP, Brazil.
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Pereira MR, Maester TC, Mercaldi GF, de Macedo Lemos EG, Hyvönen M, Balan A. From a metagenomic source to a high-resolution structure of a novel alkaline esterase. Appl Microbiol Biotechnol 2017; 101:4935-4949. [PMID: 28331945 DOI: 10.1007/s00253-017-8226-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 02/27/2017] [Accepted: 03/05/2017] [Indexed: 10/19/2022]
Abstract
Esterases catalyze the cleavage and formation of ester bonds and are members of the diverse family of α/β hydrolase fold. They are useful in industries from different sectors, such as food, detergent, fine chemicals, and biofuel production. In a previous work, 30 positive clones for lipolytic activity were identified from a metagenomic library of a microbial consortium specialized in diesel oil degradation. In this study, a putative gene encoding an esterase/lipase, denominated est8, has been cloned and the corresponding protein expressed recombinantly, purified to homogeneity and characterized functional and structurally. We show that the protein codified by est8 gene, denominated Est8, is an alkaline esterase with high catalytic efficiency against p-nitrophenyl acetate and stable in the presence of up to 10% dimethyl sulfoxide. The three-dimensional structure of Est8 was determined at 1.85-Ǻ resolution, allowing the characterization of the substrate-binding pocket and features that rationalize the preference of Est8 for short-chain substrates. In an attempt to increase the size of ligand-binding pocket and enzyme activity against distinct substrates of long chain, we mutated two residues (Met213 and Phe217) that block the substrate channel. A small increase in the reaction velocity for p-nitrophenyl butyrate and p-nitrophenyl valerate hydrolysis was observed. Activity against p-nitrophenyl acetate was reduced. The functional and structural characterization of Est8 is explored in comparison with orthologues.
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Affiliation(s)
- Mariana Rangel Pereira
- National Laboratory of Biosciences (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo State, Brazil.,University of São Paulo (USP), São Paulo, São Paulo State, Brazil.,Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State, Brazil
| | - Thaís Carvalho Maester
- University of São Paulo (USP), São Paulo, São Paulo State, Brazil.,Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State, Brazil
| | - Gustavo Fernando Mercaldi
- National Laboratory of Biosciences (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo State, Brazil.,Institute of Biology, University of Campinas, Campinas, São Paulo State, Brazil
| | | | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Balan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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