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Matić J, Akladios F, Battisti UM, Håversen L, Nain-Perez A, Füchtbauer AF, Kim W, Monjas L, Rivero AR, Borén J, Mardinoglu A, Uhlen M, Grøtli M. Sulfone-based human liver pyruvate kinase inhibitors - Design, synthesis and in vitro bioactivity. Eur J Med Chem 2024; 269:116306. [PMID: 38471358 DOI: 10.1016/j.ejmech.2024.116306] [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: 09/18/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a prevalent pathological condition characterised by the accumulation of fat in the liver. Almost one-third of the global population is affected by NAFLD, making it a significant health concern. However, despite its prevalence, there is currently no approved drug specifically designed for the treatment of NAFLD. To address this critical gap, researchers have been investigating potential targets for NAFLD drug development. One promising candidate is the liver isoform of pyruvate kinase (PKL). In recent studies, Urolithin C, an allosteric inhibitor of PKL, has emerged as a potential lead compound for therapeutic intervention. Building upon this knowledge, our team has conducted a comprehensive structure-activity relationship of Urolithin C. In this work, we have employed a scaffold-hopping approach, modifying the urolithin structure by replacing the urolithin carbonyl with a sulfone moiety. Our structure-activity relationship analysis has identified the sulfone group as particularly favourable for potent PKL inhibition. Additionally, we have found that the presence of catechol moieties on the two aromatic rings further improves the inhibitory activity. The most promising inhibitor from this new series displayed nanomolar inhibition, boasting an IC50 value of 0.07 μM. This level of potency rivals that of urolithin D and significantly surpasses the effectiveness of urolithin C by an order of magnitude. To better understand the molecular interactions underlying this inhibition, we obtained the crystal structure of one of the inhibitors complexed with PKL. This structural insight served as a valuable reference point, aiding us in the design of inhibitors.
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Affiliation(s)
- Josipa Matić
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fady Akladios
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Umberto Maria Battisti
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - Amalyn Nain-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anders Foller Füchtbauer
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Woonghee Kim
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Leticia Monjas
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Alexandra Rodriguez Rivero
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden.
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Swint-Kruse L, Dougherty LL, Page B, Wu T, O’Neil PT, Prasannan CB, Timmons C, Tang Q, Parente DJ, Sreenivasan S, Holyoak T, Fenton AW. PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) 2023; 2023:baad030. [PMID: 37171062 PMCID: PMC10176505 DOI: 10.1093/database/baad030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Larissa L Dougherty
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Braelyn Page
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Tiffany Wu
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Pierce T O’Neil
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Charulata B Prasannan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Cody Timmons
- Chemistry Department, Southwestern Oklahoma State University, 100 Campus Dr., Weatherford, OK 73096, USA
| | - Qingling Tang
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Daniel J Parente
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Family Medicine and Community Health, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Shwetha Sreenivasan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Todd Holyoak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
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Battisti UM, Monjas L, Akladios F, Matic J, Andresen E, Nagel CH, Hagkvist M, Håversen L, Kim W, Uhlen M, Borén J, Mardinoğlu A, Grøtli M. Exploration of Novel Urolithin C Derivatives as Non-Competitive Inhibitors of Liver Pyruvate Kinase. Pharmaceuticals (Basel) 2023; 16:ph16050668. [PMID: 37242451 DOI: 10.3390/ph16050668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The inhibition of liver pyruvate kinase could be beneficial to halt or reverse non-alcoholic fatty liver disease (NAFLD), a progressive accumulation of fat in the liver that can lead eventually to cirrhosis. Recently, urolithin C has been reported as a new scaffold for the development of allosteric inhibitors of liver pyruvate kinase (PKL). In this work, a comprehensive structure-activity analysis of urolithin C was carried out. More than 50 analogues were synthesized and tested regarding the chemical features responsible for the desired activity. These data could pave the way to the development of more potent and selective PKL allosteric inhibitors.
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Affiliation(s)
- Umberto Maria Battisti
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 65 Stockholm, Sweden
| | - Leticia Monjas
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 65 Stockholm, Sweden
| | - Fady Akladios
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 65 Stockholm, Sweden
| | - Josipa Matic
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 65 Stockholm, Sweden
| | - Eric Andresen
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Carolin H Nagel
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Malin Hagkvist
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
- Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 65 Stockholm, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 65 Stockholm, Sweden
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
- Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden
| | - Adil Mardinoğlu
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 65 Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
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Nain-Perez A, Nilsson O, Lulla A, Håversen L, Brear P, Liljenberg S, Hyvönen M, Borén J, Grøtli M. Tuning liver pyruvate kinase activity up or down with a new class of allosteric modulators. Eur J Med Chem 2023; 250:115177. [PMID: 36753880 DOI: 10.1016/j.ejmech.2023.115177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023]
Abstract
The liver isoform of pyruvate kinase (PKL) has gained interest due to its potential capacity to regulate fatty acid synthesis involved in the progression of non-alcoholic fatty liver disease (NAFLD). Here we describe a novel series of PKL modulators that can either activate or inhibit the enzyme allosterically, from a cryptic site at the interface of two protomers in the tetrameric enzyme. Starting from urolithin D, we designed and synthesised 42 new compounds. The effect of these compounds on PKL enzymatic activity was assessed after incubation with cell lysates obtained from a liver cell line. Pronounced activation of PKL activity, up to 3.8-fold, was observed for several compounds at 10 μM, while other compounds were prominent PKL inhibitors reducing its activity to 81% at best. A structure-activity relationship identified linear-shaped sulfone-sulfonamides as activators and non-linear compounds as inhibitors. Crystal structures revealed the conformations of these modulators, which were used as a reference for designing new modulators.
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Affiliation(s)
- Amalyn Nain-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Oscar Nilsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Sara Liljenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-413 45, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden.
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Zhang W, Sun X, Lei Y, Liu X, Zhang Y, Wang Y, Lin H. Roles of selenoprotein K in oxidative stress and endoplasmic reticulum stress under selenium deficiency in chicken liver. Comp Biochem Physiol C Toxicol Pharmacol 2023; 264:109504. [PMID: 36375805 DOI: 10.1016/j.cbpc.2022.109504] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
Selenoprotein K (SELENOK) is a major part of selenoprotein family. Selenoproteins have been proven playing vital roles in a variety of physiological processes. However, as a necessary supplement to the body of trace elements, how SELENOK regulates necroptosis in chicken liver has none clear claim. The purpose of this study was to cover the mechanism of SELENOK act in necroptosis of chicken liver. By feeding Se-deficiency diet for 1-day-old hyline chickens, we successfully built SELENOK-deficiency and discussed the regulation SELENOK have done. The test of liver function showed there has dysfunction appeared in the -Se groups. Results of TEM showed necroptosis occurred in the 35-Se group. After that western blot and qRT-PCR results prompted us SELENOK-deficiency caused large accumulation of ROS, enhanced endoplasmic reticulum stress, abnormally elevated HSPs family expression, and activated RIPK1-RIPK3 complex. In order to show the regulation of SELENOK in chicken liver, we artificially knocked off SELENOK gene in LMH cells. Through AO/EB staining we also found necroptosis in the siRNA-Se group. Furthermore, the results in LMH cells were coincided with those in chicken (Gallus gallus) liver. Our experiment clarified the molecular mechanism of SELENOK in the regulation and liver necroptosis, and provided reference for the healthy feeding mode of broilers.
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Affiliation(s)
- Wenyue Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Xinyue Sun
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Yutian Lei
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiaojing Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Yilei Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Yuqi Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Hongjin Lin
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of the Provincial Education, Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China.
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Liao Y, Davies NA, Bogle IDL. A process systems Engineering approach to analysis of fructose consumption in the liver system and consequences for Non-Alcoholic fatty liver disease. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Reductive elimination of alkoxy group in anthraquinone derivatives. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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