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He Y, Zhou L, Wang M, Zhong Z, Chen H, Lian C, Zhang H, Wang H, Cao L, Li C. Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134612. [PMID: 38761766 DOI: 10.1016/j.jhazmat.2024.134612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/27/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms.
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Affiliation(s)
- Yameng He
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Zhou
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Minxiao Wang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhaoshan Zhong
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Chen
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chao Lian
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Wang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lei Cao
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 10049, China; Laoshan Laboratory, Qingdao 266237, China.
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2
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Glover RG, Soulsby DP. One-pot Dess-Martin periodinane-mediated oxidative deprotection and olefination of trimethylsilyl-protected pyranosides and pyranoses. Carbohydr Res 2023; 532:108904. [PMID: 37517196 DOI: 10.1016/j.carres.2023.108904] [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: 06/04/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
The selective functionalization of carbohydrates provides a powerful method for introducing structural complexity, allowing access to unique drug scaffolds with distinctive pharmaceutical profiles. Herein, we describe an efficient and selective carbon-carbon bond forming reaction of a variety of common trimethylsilyl-protected pyranosides and pyranoses at C-6 using a one-pot Dess-Martin periodinane-mediated oxidation deprotection. This is followed by addition of stabilized and non-stabilized ylides to generate alkenoate carbohydrates and related analogs in good to moderate yields. We also report on the rapid deprotection of the remaining trimethylsilyl ether groups in near quantitative yields using an acidic resin-mediated ethanolysis.
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Affiliation(s)
- Rowan G Glover
- Department of Chemistry, University of Redlands, 1200 E. Colton Avenue, Redlands, CA, 92374, USA
| | - David P Soulsby
- Department of Chemistry, University of Redlands, 1200 E. Colton Avenue, Redlands, CA, 92374, USA.
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3
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Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A. Molecules 2021; 26:molecules26020320. [PMID: 33435514 PMCID: PMC7827217 DOI: 10.3390/molecules26020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5'-position or 3'-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5'-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors.
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Gresh N, Perahia D, de Courcy B, Foret J, Roux C, El-Khoury L, Piquemal JP, Salmon L. Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown. J Comput Chem 2016; 37:2770-2782. [DOI: 10.1002/jcc.24503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale; Paris France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées (LBPA), UMR 8113; Ecole Normale Supérieure Cachan France
| | - Benoit de Courcy
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale; Paris France
| | - Johanna Foret
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
| | - Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
| | - Lea El-Khoury
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Centre d'Analyses et de Recherche; UR EGFEM, LSIM, Faculté de Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Department of Biomolecular Engineering; The University of Texas at Austin; Texas 78712
| | - Laurent Salmon
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
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5
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Nizamov IS, Nikitin YN, Nizamov ID, Belov TG, Voloshina AD, Batyeva ES, Cherkasov RA. α-d-Glucofuranose and α-d-allofuranose diacetonides and silyl ether of α-d-glucofuranose diacetonide in dithiophosphorylation reactions. HETEROATOM CHEMISTRY 2016. [DOI: 10.1002/hc.21344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ilyas S. Nizamov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Kazan Russia
| | - Yevgeniy N. Nikitin
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
| | - Ilnar D. Nizamov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
| | - Timur G. Belov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
| | - Alexandra D. Voloshina
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Kazan Russia
| | - Elvira S. Batyeva
- State Budgetary-Funded Institution of Science A.E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Center of Russian Academy of Sciences; Kazan Russia
| | - Rafael A. Cherkasov
- A.M. Butlerov Institute of Chemistry; Kazan (Volga region) Federal University; Kazan Russia
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Cai M, Hruby VJ. The Melanocortin Receptor System: A Target for Multiple Degenerative Diseases. Curr Protein Pept Sci 2016; 17:488-96. [PMID: 26916163 DOI: 10.2174/1389203717666160226145330] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 01/28/2016] [Accepted: 01/08/2016] [Indexed: 01/10/2023]
Abstract
The melanocortin receptor system consists of five closely related G-protein coupled receptors (MC1R, MC2R, MC3R, MC4R and MC5R). These receptors are involved in many of the key biological functions for multicellular animals, including human beings. The natural agonist ligands for these receptors are derived by processing of a primordial animal gene product, proopiomelanocortin (POMC). The ligand for the MC2R is ACTH (Adrenal Corticotropic Hormone), a larger processed peptide from POMC. The natural ligands for the other 4 melanocortin receptors are smaller peptides including α-melanocyte stimulating hormone (α-MSH) and related peptides from POMC (β-MSH and γ-MSH). They all contain the sequence His-Phe-Arg-Trp that is conserved throughout evolution. Thus, there has been considerable difficulty in developing highly selective ligands for the MC1R, MC3R, MC4R and MC5R. In this brief review, we discuss the various approaches that have been taken to design agonist and antagonist analogues and derivatives of the POMC peptides that are selective for the MC1R, MC3R, MC4R and MC5R receptors, via peptide, nonpeptide and peptidomimetic derivatives and analogues and their differential interactions with receptors that may help account for these selectivities.
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Affiliation(s)
| | - Victor J Hruby
- Department of Chemistry & Biochemistry, University of Arizona, 1306 E. University Blvd, Tucson, AZ 85721, USA.
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Shi Y, Ren P, Schnieders M, Piquemal JP. Polarizable Force Fields for Biomolecular Modeling. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Development of new chiral ligand exchange capillary electrophoresis system with amino acid ionic liquids ligands and its application in studying the kinetics of l-amino acid oxidase. Anal Chim Acta 2014; 821:97-102. [DOI: 10.1016/j.aca.2014.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/04/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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9
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Ludin P, Woodcroft B, Ralph SA, Mäser P. In silico prediction of antimalarial drug target candidates. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2012; 2:191-9. [PMID: 24533280 DOI: 10.1016/j.ijpddr.2012.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/28/2012] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
Abstract
The need for new antimalarials is persistent due to the emergence of drug resistant parasites. Here we aim to identify new drug targets in Plasmodium falciparum by phylogenomics among the Plasmodium spp. and comparative genomics to Homo sapiens. The proposed target discovery pipeline is largely independent of experimental data and based on the assumption that P. falciparum proteins are likely to be essential if (i) there are no similar proteins in the same proteome and (ii) they are highly conserved across the malaria parasites of mammals. This hypothesis was tested using sequenced Saccharomycetaceae species as a touchstone. Consecutive filters narrowed down the potential target space of P. falciparum to proteins that are likely to be essential, matchless in the human proteome, expressed in the blood stages of the parasite, and amenable to small molecule inhibition. The final set of 40 candidate drug targets was significantly enriched in essential proteins and comprised proven targets (e.g. dihydropteroate synthetase or enzymes of the non-mevalonate pathway), targets currently under investigation (e.g. calcium-dependent protein kinases), and new candidates of potential interest such as phosphomannose isomerase, phosphoenolpyruvate carboxylase, signaling components, and transporters. The targets were prioritized based on druggability indices and on the availability of in vitro assays. Potential inhibitors were inferred from similarity to known targets of other disease systems. The identified candidates from P. falciparum provide insight into biochemical peculiarities and vulnerable points of the malaria parasite and might serve as starting points for rational drug discovery.
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Affiliation(s)
- Philipp Ludin
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland ; University of Basel, 4000 Basel, Switzerland
| | - Ben Woodcroft
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland ; University of Basel, 4000 Basel, Switzerland
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Desvergnes S, Courtiol-Legourd S, Daher R, Dabrowski M, Salmon L, Therisod M. Synthesis and evaluation of malonate-based inhibitors of phosphosugar-metabolizing enzymes: class II fructose-1,6-bis-phosphate aldolases, type I phosphomannose isomerase, and phosphoglucose isomerase. Bioorg Med Chem 2012; 20:1511-20. [PMID: 22269276 DOI: 10.1016/j.bmc.2011.12.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 11/29/2022]
Abstract
In the design of inhibitors of phosphosugar metabolizing enzymes and receptors with therapeutic interest, malonate has been reported in a number of cases as a good and hydrolytically-stable surrogate of the phosphate group, since both functions are dianionic at physiological pH and of comparable size. We have investigated a series of malonate-based mimics of the best known phosphate inhibitors of class II (zinc) fructose-1,6-bis-phosphate aldolases (FBAs) (e.g., from Mycobacterium tuberculosis), type I (zinc) phosphomannose isomerase (PMI) from Escherichia coli, and phosphoglucose isomerase (PGI) from yeast. In the case of FBAs, replacement of one phosphate by one malonate on a bis-phosphorylated inhibitor (1) led to a new compound (4) still showing a strong inhibition (K(i) in the nM range) and class II versus class I selectivity (up to 8×10(4)). Replacement of the other phosphate however strongly affected binding efficiency and selectivity. In the case of PGI and PMI, 5-deoxy-5-malonate-D-arabinonohydroxamic acid (8) yielded a strong decrease in binding affinities when compared to its phosphorylated parent compound 5-phospho-D-arabinonohydroxamic acid (2). Analysis of the deposited 3D structures of the kinetically evaluated enzymes complexed to the phosphate-based inhibitors indicate that malonate could be a good phosphate surrogate only if phosphate is not tightly bound at the enzyme active site, such as in position 7 of compound 1 for FBAs. These observations are of importance for further design of inhibitors of phosphorylated-compounds metabolizing enzymes with therapeutic interest.
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Affiliation(s)
- Stéphanie Desvergnes
- Univ. Paris-Sud, Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, UMR8182, LabEx LERMIT, Orsay F-91405, France
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11
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Yeom SJ, Kim YS, Lim YR, Jeong KW, Lee JY, Kim Y, Oh DK. Molecular characterization of a novel thermostable mannose-6-phosphate isomerase from Thermus thermophilus. Biochimie 2011; 93:1659-67. [PMID: 21729734 DOI: 10.1016/j.biochi.2011.05.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 05/24/2011] [Indexed: 11/25/2022]
Abstract
Mannose-6-phosphate isomerase catalyzes the interconversion of mannose-6-phosphate and fructose-6-phosphate. The gene encoding a putative mannose-6-phosphate isomerase from Thermus thermophilus was cloned and expressed in Escherichia coli. The native enzyme was a 29 kDa monomer with activity maxima for mannose 6-phosphate at pH 7.0 and 80 °C in the presence of 0.5 mM Zn(2+) that was present at one molecule per monomer. The half-lives of the enzyme at 65, 70, 75, 80, and 85 °C were 13, 6.5, 3.7, 1.8, and 0.2 h, respectively. The 15 putative active-site residues within 4.5 Å of the substrate mannose 6-phosphate in the homology model were individually replaced with other amino acids. The sequence alignments, activities, and kinetic analyses of the wild-type and mutant enzymes with amino acid changes at His50, Glu67, His122, and Glu132 as well as homology modeling suggested that these four residues are metal-binding residues and may be indirectly involved in catalysis. In the model, Arg11, Lys37, Gln48, Lys65 and Arg142 were located within 3 Å of the bound mannose 6-phosphate. Alanine substitutions of Gln48 as well as Arg142 resulted in increase of K(m) and dramatic decrease of k(cat), and alanine substitutions of Arg11, Lys37, and Lys65 affected enzyme activity. These results suggest that these 5 residues are substrate-binding residues. Although Trp13 was located more than 3 Å from the substrate and may not interact directly with substrate or metal, the ring of Trp13 was essential for enzyme activity.
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Affiliation(s)
- Soo-Jin Yeom
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hayang-dong, Gangjin-gu, Seoul 143-701, Republic of Korea
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12
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Gresh N, de Courcy B, Piquemal JP, Foret J, Courtiol-Legourd S, Salmon L. Polarizable Water Networks in Ligand–Metalloprotein Recognition. Impact on the Relative Complexation Energies of Zn-Dependent Phosphomannose Isomerase with d-Mannose 6-Phosphate Surrogates. J Phys Chem B 2011; 115:8304-16. [DOI: 10.1021/jp2024654] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR8601 CNRS, Univ Paris Descartes, UFR Biomédicale, Faculté de Médecine de Paris, F-75006, Paris, France
| | - Benoit de Courcy
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR8601 CNRS, Univ Paris Descartes, UFR Biomédicale, Faculté de Médecine de Paris, F-75006, Paris, France
- Laboratoire de Chimie Théorique, UPMC Univ Paris 06, UMR7616, F-75252, Paris, France
- Laboratoire de Chimie Théorique, CNRS, UMR7616, F-75252, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UPMC Univ Paris 06, UMR7616, F-75252, Paris, France
- Laboratoire de Chimie Théorique, CNRS, UMR7616, F-75252, Paris, France
| | - Johanna Foret
- Laboratoire de Chimie Bioorganique et Bioinorganique, Univ Paris-Sud, ICMMO, UMR8182, F-91405, Orsay, France
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS, ICMMO, UMR8182, F-91405, Orsay, France
| | - Stéphanie Courtiol-Legourd
- Laboratoire de Chimie Bioorganique et Bioinorganique, Univ Paris-Sud, ICMMO, UMR8182, F-91405, Orsay, France
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS, ICMMO, UMR8182, F-91405, Orsay, France
| | - Laurent Salmon
- Laboratoire de Chimie Bioorganique et Bioinorganique, Univ Paris-Sud, ICMMO, UMR8182, F-91405, Orsay, France
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS, ICMMO, UMR8182, F-91405, Orsay, France
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Roux C, Bhatt F, Foret J, de Courcy B, Gresh N, Piquemal JP, Jeffery CJ, Salmon L. The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins 2011; 79:203-20. [PMID: 21058398 DOI: 10.1002/prot.22873] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Type I phosphomannose isomerases (PMIs) are zinc-dependent metalloenzymes involved in the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P). 5-Phospho-D-arabinonohydroxamic acid (5PAH), an inhibitor endowed with nanomolar affinity for yeast (Type I) and Pseudomonas aeruginosa (Type II) PMIs (Roux et al., Biochemistry 2004; 43:2926-2934), strongly inhibits human (Type I) PMI (for which we report an improved expression and purification procedure), as well as Escherichia coli (Type I) PMI. Its K(i) value of 41 nM for human PMI is the lowest value ever reported for an inhibitor of PMI. 5-Phospho-D-arabinonhydrazide, a neutral analogue of the reaction intermediate 1,2-cis-enediol, is about 15 times less efficient at inhibiting both enzymes, in accord with the anionic nature of the postulated high-energy reaction intermediate. Using the polarizable molecular mechanics, sum of interactions between fragments ab initio computed (SIBFA) procedure, computed structures of the complexes between Candida albicans (Type I) PMI and the cyclic substrate β-D-mannopyranose 6-phosphate (β-M6P) and between the enzyme and the high-energy intermediate analogue inhibitor 5PAH are reported. Their analysis allows us to identify clearly the nature of each individual active site amino acid and to formulate a hypothesis for the overall mechanism of the reaction catalyzed by Type I PMIs, that is, the ring-opening and isomerization steps, respectively. Following enzyme-catalyzed ring-opening of β-M6P by zinc-coordinated water and Gln111 ligands, Lys136 is identified as the probable catalytic base involved in proton transfer between the two carbon atoms C1 and C2 of the substrate D-mannose 6-phosphate.
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Affiliation(s)
- Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
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14
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Dahl R, Bravo Y, Sharma V, Ichikawa M, Dhanya RP, Hedrick M, Brown B, Rascon J, Vicchiarelli M, Mangravita-Novo A, Yang L, Stonich D, Su Y, Smith LH, Sergienko E, Freeze HH, Cosford NDP. Potent, selective, and orally available benzoisothiazolone phosphomannose isomerase inhibitors as probes for congenital disorder of glycosylation Ia. J Med Chem 2011; 54:3661-8. [PMID: 21539312 DOI: 10.1021/jm101401a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report the discovery and validation of a series of benzoisothiazolones as potent inhibitors of phosphomannose isomerase (PMI), an enzyme that converts mannose-6-phosphate (Man-6-P) into fructose-6-phosphate (Fru-6-P) and, more importantly, competes with phosphomannomutase 2 (PMM2) for Man-6-P, diverting this substrate from critical protein glycosylation events. In congenital disorder of glycosylation type Ia, PMM2 activity is compromised; thus, PMI inhibition is a potential strategy for the development of therapeutics. High-throughput screening (HTS) and subsequent chemical optimization led to the identification of a novel class of benzoisothiazolones as potent PMI inhibitors having little or no PMM2 inhibition. Two complementary synthetic routes were developed, enabling the critical structural requirements for activity to be determined, and the compounds were subsequently profiled in biochemical and cellular assays to assess efficacy. The most promising compounds were also profiled for bioavailability parameters, including metabolic stability, plasma stability, and permeability. The pharmacokinetic profile of a representative of this series (compound 19; ML089) was also assessed, demonstrating the potential of this series for in vivo efficacy when dosed orally in disease models.
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Affiliation(s)
- Russell Dahl
- Apoptosis and Cell Death Research Program, Conrad Prebys Center for Chemical Genomics, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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15
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Devereux M, van Severen MC, Parisel O, Piquemal JP, Gresh N. Role of Cation Polarization in holo- and hemi-Directed [Pb(H2O)n]2+ Complexes and Development of a Pb2+ Polarizable Force Field. J Chem Theory Comput 2010; 7:138-47. [DOI: 10.1021/ct1004005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mike Devereux
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Marie-Céline van Severen
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Olivier Parisel
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Nohad Gresh
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
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Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J. Analysis of the Interactions Taking Place in the Recognition Site of a Bimetallic Mg(II)−Zn(II) Enzyme, Isopentenyl Diphosphate Isomerase. A Parallel Quantum-Chemical and Polarizable Molecular Mechanics Study. J Phys Chem B 2010; 114:4884-95. [DOI: 10.1021/jp907629k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Nicole Audiffren
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jerome de Ruyck
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Marie Ledecq
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Johan Wouters
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
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